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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:07:10
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.40.0
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+Version: 1.41.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:07:10
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.39.0
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+Version: 1.40.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:32
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.38.0
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+Version: 1.39.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:32
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.37.0
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+Version: 1.38.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:03:53
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.36.0
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+Version: 1.37.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:03:53
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.35.0
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+Version: 1.36.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:53:08
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.34.0
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+Version: 1.35.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:53:08
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.33.0
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+Version: 1.34.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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simplify email address

Michael Lawrence authored on 05/01/2021 19:14:02
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@@ -1,5 +1,5 @@
1 1
 Package: gmapR
2
-Maintainer: Michael Lawrence <lawrence.michael@gene.com>
2
+Maintainer: Michael Lawrence <michafla@gene.com>
3 3
 License: Artistic-2.0
4 4
 Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
5 5
 Type: Package
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bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:46:29
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.32.0
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+Version: 1.33.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:46:29
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.31.0
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+Version: 1.32.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:30:24
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.30.0
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+Version: 1.31.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:30:24
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.29.0
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+Version: 1.30.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:36:17
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.28.0
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+Version: 1.29.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:33
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.27.2
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+Version: 1.28.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.27.1
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+Version: 1.27.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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update GSTRUCT source code

Michael Lawrence authored on 22/05/2019 19:39:45
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.27.0
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+Version: 1.27.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:13
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.26.0
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+Version: 1.27.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:37
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.25.3
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+Version: 1.26.0
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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embed samtools sources directly, since Rsamtools has moved to htslib

Michael Lawrence authored on 11/02/2019 20:33:07
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.25.2
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+Version: 1.25.3
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bam tally no longer crashes when NM exceeds maximum bin

Michael Lawrence authored on 05/02/2019 19:11:42
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.25.1
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+Version: 1.25.2
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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version bump

Michael Lawrence authored on 20/11/2018 19:02:28
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.25.0
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+Version: 1.25.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:30
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.24.0
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+Version: 1.25.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:49
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.23.1
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+Version: 1.24.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:49:42
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.23.0
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+Version: 1.23.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:39
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.22.0
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+Version: 1.23.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 15
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:25
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.21.3
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+Version: 1.22.0
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:24:43
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@@ -9,13 +9,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.21.2
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+Version: 1.21.3
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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-        GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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-Imports: S4Vectors (>= 0.13.13), IRanges, BiocGenerics (>= 0.25.1),
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-        rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
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-        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
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-        GenomicAlignments (>= 1.1.9), BiocParallel
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+        GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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+Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
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+        rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings,
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+        VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome,
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+        GenomicAlignments (>= 1.15.6), BiocParallel
19 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
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         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
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The path() generic has moved from Rsamtools to BiocGenerics

LiNk-NY authored on 20/12/2017 20:04:28
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@@ -9,10 +9,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.21.1
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+Version: 1.21.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15
-Imports: S4Vectors (>= 0.13.13), IRanges, 
15
+Imports: S4Vectors (>= 0.13.13), IRanges, BiocGenerics (>= 0.25.1),
16 16
         rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
17 17
         VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
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         GenomicAlignments (>= 1.1.9), BiocParallel
Browse code

version bump

Michael Lawrence authored on 14/11/2017 23:02:49
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.21.0
12
+Version: 1.21.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.13.13), IRanges, 
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bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:20
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.20.0
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+Version: 1.21.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.13.13), IRanges, 
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bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:47
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.19.2
12
+Version: 1.20.0
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.13.13), IRanges, 
Browse code

fixes for keep_ref=TRUE

Michael Lawrence authored on 14/09/2017 18:30:38
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.19.1
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+Version: 1.19.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.13.13), IRanges, 
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@129718 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 18/05/2017 22:47:55
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.19.0
12
+Version: 1.19.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.13.13), IRanges, 
Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.18.0
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+Version: 1.19.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.13.13), IRanges, 
Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.17.2
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+Version: 1.18.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.13.13), IRanges, 
Browse code

follow renaming of union classes in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@126394 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 01/02/2017 13:23:02
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@@ -9,10 +9,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.17.1
12
+Version: 1.17.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15
-Imports: S4Vectors (>= 0.9.25), IRanges, 
15
+Imports: S4Vectors (>= 0.13.13), IRanges, 
16 16
         rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
17 17
         VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
18 18
         GenomicAlignments (>= 1.1.9), BiocParallel
Browse code

start on C-level interface to IIT files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@125153 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/12/2016 18:20:54
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@@ -24,10 +24,10 @@ Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
24 24
         GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
25 25
         GmapParam-class.R GsnapParam-class.R
26 26
         GsnapOutput-class.R GmapOutput-class.R
27
-        atoiindex-command.R
27
+        atoiindex-command.R iit-format.R
28 28
         BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
29 29
         get-genome-command.R gmap-command.R gmap_build-command.R
30
-        gsnap-command.R iit-format.R iit_store-command.R info.R
30
+        gsnap-command.R iit_store-command.R info.R
31 31
         snpindex-command.R system.R test_gmapR_package.R
32 32
         makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
33 33
 biocViews: Alignment
Browse code

update to latest GSTRUCT

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@123972 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/11/2016 21:54:30
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.17.0
12
+Version: 1.17.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.16.0
12
+Version: 1.17.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.15.0
12
+Version: 1.16.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.14.0
12
+Version: 1.15.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.11
12
+Version: 1.14.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

adjustments in response to the vals -> filter renaming in GenomicFeatures

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@115831 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/04/2016 22:55:27
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.10
12
+Version: 1.13.11
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, 
Browse code

move Rsamtools to Depends to avoid masking of bamPaths()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@114675 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 12/03/2016 19:23:55
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@@ -11,8 +11,8 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
11 11
         per-nucleotide basis using the bam_tally tool.
12 12
 Version: 1.13.10
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14
-        GenomicRanges (>= 1.17.12)
15
-Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),
14
+        GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15
+Imports: S4Vectors (>= 0.9.25), IRanges, 
16 16
         rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
17 17
         VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
18 18
         GenomicAlignments (>= 1.1.9), BiocParallel
Browse code

stream past XS counts for indels (even when XS counting is disabled)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@113152 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 01/02/2016 20:11:05
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.9
12
+Version: 1.13.10
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),
Browse code

elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@113044 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/01/2016 01:22:03
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@@ -9,12 +9,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.8
12
+Version: 1.13.9
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
15
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
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-        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
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-        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
15
+Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),
16
+        rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
17
+        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
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+        GenomicAlignments (>= 1.1.9), BiocParallel
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 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
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         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
Browse code

make seqinfo setting robust to missing seqlevels

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111247 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/12/2015 03:40:40
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.7
12
+Version: 1.13.8
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
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 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
Browse code

fix single output case for GMAP

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111240 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 05/12/2015 15:00:00
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.6
12
+Version: 1.13.7
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
Browse code

general cleanup and fixes, doc updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111183 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 03/12/2015 21:11:09
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.5
12
+Version: 1.13.6
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
Browse code

add raw total count statistic to tallies (everything else now qual filtered)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110891 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 24/11/2015 22:19:59
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.4
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+Version: 1.13.5
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
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 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
Browse code

add ability to call GMAP

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110840 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/11/2015 23:25:34
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@@ -9,10 +9,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.3
12
+Version: 1.13.4
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
15
+Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
16 16
         GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
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         tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
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 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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@@ -21,7 +21,9 @@ Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         LungCancerLines
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 Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
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         GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
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-        GsnapParam-class.R GsnapOutput-class.R atoiindex-command.R
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+        GmapParam-class.R GsnapParam-class.R
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+        GsnapOutput-class.R GmapOutput-class.R
26
+        atoiindex-command.R
25 27
         BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
26 28
         get-genome-command.R gmap-command.R gmap_build-command.R
27 29
         gsnap-command.R iit-format.R iit_store-command.R info.R
Browse code

add untested support for FaFile=>GmapGenome

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110737 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 19/11/2015 18:51:30
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.2
12
+Version: 1.13.3
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

work towards supporting new bam_tally; drops quality info (now cutoff based), adds xs/nm/del and codon-level counts

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110593 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/11/2015 21:50:11
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.1
12
+Version: 1.13.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

resurrect improvements that we reverted before the April release, expect breakage for a while

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 18:51:00
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.13.0
12
+Version: 1.13.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.12.0
12
+Version: 1.13.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.11.1
12
+Version: 1.12.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

labeledLine() was moved from BiocGenerics to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@107244 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/08/2015 23:37:20
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.11.0
12
+Version: 1.11.1
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.10.0
12
+Version: 1.11.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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... ...
@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.9.1
12
+Version: 1.10.0
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Reverted to r101133, along with NAMESPACE fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:40:44
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... ...
@@ -9,13 +9,12 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.9.2
13
-Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges
14
-        (>= 1.17.12)
15
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>=
16
-        1.25.5), GenomicFeatures (>= 1.17.13), Biostrings,
17
-        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
18
-        GenomicAlignments (>= 1.1.9), BiocParallel
12
+Version: 1.9.1
13
+Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14
+        GenomicRanges (>= 1.17.12)
15
+Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
16
+        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
17
+        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
19 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
20 19
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
21 20
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
... ...
@@ -29,4 +28,3 @@ Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
29 28
         snpindex-command.R system.R test_gmapR_package.R
30 29
         makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
31 30
 biocViews: Alignment
32
-Packaged: 2015-04-14 02:31:15 UTC; beckerg4
Browse code

Recent work towards supporting the new features... will revert back to a stable version immediately...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102485 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:32:10
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... ...
@@ -10,11 +10,12 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12 12
 Version: 1.9.2
13
-Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14
-        GenomicRanges (>= 1.17.12)
15
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
16
-        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
17
-        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
13
+Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges
14
+        (>= 1.17.12)
15
+Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>=
16
+        1.25.5), GenomicFeatures (>= 1.17.13), Biostrings,
17
+        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
18
+        GenomicAlignments (>= 1.1.9), BiocParallel
18 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 20
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
20 21
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
... ...
@@ -28,3 +29,4 @@ Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
28 29
         snpindex-command.R system.R test_gmapR_package.R
29 30
         makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
30 31
 biocViews: Alignment
32
+Packaged: 2015-04-14 02:31:15 UTC; beckerg4
Browse code

update gstruct/bamtally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101176 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 25/03/2015 20:25:05
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
9 9
         methods to work with GMAP and GSNAP from within R. In addition,
10 10
         it provides methods to tally alignment results on a
11 11
         per-nucleotide basis using the bam_tally tool.
12
-Version: 1.9.1
12
+Version: 1.9.2
13 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 14
         GenomicRanges (>= 1.17.12)
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

fix broken Fasta->GmapGenome export example

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@98087 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 06/01/2015 23:00:23
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@@ -1,8 +1,7 @@
1 1
 Package: gmapR
2 2
 Maintainer: Michael Lawrence <lawrence.michael@gene.com>
3 3
 License: Artistic-2.0
4
-Title: Provides convenience methods to work with GMAP and GSNAP from
5
-        within R
4
+Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
6 5
 Type: Package
7 6
 Author: Cory Barr, Thomas Wu, Michael Lawrence
8 7
 Description: GSNAP and GMAP are a pair of tools to align short-read
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@@ -10,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 9
         methods to work with GMAP and GSNAP from within R. In addition,
11 10
         it provides methods to tally alignment results on a
12 11
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.9.0
12
+Version: 1.9.1
14 13
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 14
         GenomicRanges (>= 1.17.12)
16 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.8.0
13
+Version: 1.9.0
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.8
13
+Version: 1.8.0
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

version bump to deploy previous bugfix

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93750 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 02/09/2014 22:42:09
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.7
13
+Version: 1.7.8
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

some fiddling, disable maintainer mode, vbump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93390 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 14/08/2014 20:39:03
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.6
13
+Version: 1.7.7
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
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@@ -15,7 +15,7 @@ Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
17 17
         GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
18
-        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9)
18
+        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
19 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
20 20
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
21 21
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
Browse code

follow renaming of TranscriptDb class -> TxDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@92976 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/07/2014 23:15:59
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@@ -10,11 +10,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.5
13
+Version: 1.7.6
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
17
-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.4),
17
+        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
18 18
         tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9)
19 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
20 20
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
Browse code

update to new bam_tally with support for XS counting, which we now support via BamTallyParam@count_xs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@90225 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/05/2014 02:04:05
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.4
13
+Version: 1.7.5
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

bam_tally has reworked memory management to avoid memory "leaks" that seem to happen on our cluster

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89935 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 05/05/2014 21:02:45
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.3
13
+Version: 1.7.4
14 14
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15 15
         GenomicRanges (>= 1.17.12)
16 16
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
Browse code

resync with latest changes in GenomicRanges/GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89880 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 02/05/2014 23:12:32
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@@ -11,10 +11,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13 13
 Version: 1.7.3
14
-Depends: R (>= 2.15.0), methods, GenomicRanges
15
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
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-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),
17
-        tools, Biobase, BSgenome, GenomicAlignments
14
+Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
15
+        GenomicRanges (>= 1.17.12)
16
+Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
17
+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.4),
18
+        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9)
18 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 20
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
20 21
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
Browse code

re-add counting of unique read positions (convenient when dupes are not marked) and fix an uninitialized value (param.cycle_breaks) detected by valgrind

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89842 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/05/2014 12:51:58
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... ...
@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.2
13
+Version: 1.7.3
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),
Browse code

resync with stuff moving from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89179 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/04/2014 15:04:25
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... ...
@@ -10,10 +10,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.1
13
+Version: 1.7.2
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15
-Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
15
+Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),
17 17
         tools, Biobase, BSgenome, GenomicAlignments
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 19
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
Browse code

disable read length guessing; just expect the user to provide it when they need the statistics that depend on it

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88928 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2014 19:50:15
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... ...
@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.7.0
13
+Version: 1.7.1
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.6.0
13
+Version: 1.7.0
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
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... ...
@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.5.15
13
+Version: 1.6.0
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88417 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 04/04/2014 13:36:22
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... ...
@@ -10,11 +10,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.5.14
13
+Version: 1.5.15
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
17
-        tools, Biobase, BSgenome
17
+        tools, Biobase, BSgenome, GenomicAlignments
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 19
         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
20 20
         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
Browse code

update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88343 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/04/2014 22:03:40
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.5.13
13
+Version: 1.5.14
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

cleanup gmap_build interface, add 'circular' support (automatically derived from BSgenome) and turn off chromosome sorting by default

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88309 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/04/2014 12:59:22
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.5.12
13
+Version: 1.5.13
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

TP53 genome is now named by the TxDb package from which the TP53 region was retrieved, so that it is automatically refreshed with annotation changes, and devel and release can coexist.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@87282 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 10/03/2014 23:10:51
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
         methods to work with GMAP and GSNAP from within R. In addition,
11 11
         it provides methods to tally alignment results on a
12 12
         per-nucleotide basis using the bam_tally tool.
13
-Version: 1.5.11
13
+Version: 1.5.12
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
Browse code

modify to new biocViews to DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@87035 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 04/03/2014 22:12:21
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@@ -2,47 +2,29 @@ Package: gmapR
2 2
 Maintainer: Michael Lawrence <lawrence.michael@gene.com>
3 3
 License: Artistic-2.0
4 4
 Title: Provides convenience methods to work with GMAP and GSNAP from
5
-    within R
5
+        within R
6 6
 Type: Package
7 7
 Author: Cory Barr, Thomas Wu, Michael Lawrence
8 8
 Description: GSNAP and GMAP are a pair of tools to align short-read
9
-    data written by Tom Wu.  This package provides convenience methods
10
-    to work with GMAP and GSNAP from within R. In addition, it provides 
11
-    methods to tally alignment results on a per-nucleotide basis using 
12
-    the bam_tally tool.
13
-Version: 1.5.10
9
+        data written by Tom Wu.  This package provides convenience
10
+        methods to work with GMAP and GSNAP from within R. In addition,
11
+        it provides methods to tally alignment results on a
12
+        per-nucleotide basis using the bam_tally tool.
13
+Version: 1.5.11
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
-         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
17
-         Biobase, BSgenome
16
+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
17
+        tools, Biobase, BSgenome
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19
-	  BSgenome.Scerevisiae.UCSC.sacCer3,
20
-          org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
21
-          BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
22
-License: Artistic-2.0
23
-Collate: GmapBamReader-class.R
24
-         GmapGenomeDirectory-class.R
25
-         GmapGenome-class.R
26
-         GmapSnpDirectory-class.R
27
-         GmapSnps-class.R
28
-         GsnapParam-class.R
29
-         GsnapOutput-class.R
30
-         atoiindex-command.R
31
-	 BamTallyParam-class.R
32
-         bam_tally-command.R
33
-         cmetindex-command.R
34
-         get-genome-command.R
35
-         gmap-command.R
36
-         gmap_build-command.R
37
-         gsnap-command.R
38
-         iit-format.R
39
-         iit_store-command.R
40
-         info.R
41
-         snpindex-command.R
42
-         system.R
43
-         test_gmapR_package.R
44
-         makeGmapGenomePackage.R
45
-         TP53Genome.R
46
-         utils.R
47
-	 asSystemCall.R
48
-         
19
+        BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
20
+        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
21
+        LungCancerLines
22
+Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
23
+        GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
24
+        GsnapParam-class.R GsnapOutput-class.R atoiindex-command.R
25
+        BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
26
+        get-genome-command.R gmap-command.R gmap_build-command.R
27
+        gsnap-command.R iit-format.R iit_store-command.R info.R
28
+        snpindex-command.R system.R test_gmapR_package.R
29
+        makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
30
+biocViews: Alignment
Browse code

TallyIIT object gains a 'bam' slot, of type BamFile, which is currently used for tracking the seqinfo.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86908 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/02/2014 04:44:51
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.9
13
+Version: 1.5.10
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86860 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/02/2014 23:13:55
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.8
13
+Version: 1.5.9
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

drop unique read position count and mean/variance of read positions from statistics output by bam_tally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86546 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 18/02/2014 21:24:22
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.7
13
+Version: 1.5.8
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

clip_overlaps should be clip_overlap

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86371 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 12/02/2014 17:13:58
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.6
13
+Version: 1.5.7
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

add calculation of median-distance-from-nearest-end to variantSummary()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86188 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/02/2014 01:07:22
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.5
13
+Version: 1.5.6
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

update bam_tally source for fix to quality tabulation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@85550 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 15/01/2014 21:39:44
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.4
13
+Version: 1.5.5
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

update bam_tally to fix counting issue with some range-restricted queries

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@85510 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/01/2014 19:15:57
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.3
13
+Version: 1.5.4
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

better to not import readBamGappedAlignments at all (it's defunct)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@83107 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/11/2013 22:10:44
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@@ -12,9 +12,8 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
12 12
     the bam_tally tool.
13 13
 Version: 1.5.3
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15
-Imports: IRanges, Rsamtools (>= 1.7.4), GenomicAlignments,
16
-         rtracklayer (>= 1.17.15), GenomicFeatures,
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-         Biostrings, VariantAnnotation (>= 1.9.4), tools,
15
+Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
+         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
18 17
          Biobase, BSgenome
19 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
20 19
 	  BSgenome.Scerevisiae.UCSC.sacCer3,
Browse code

Import readGAlignmentsFromBam from new GenomicAlignments package instead of Rsamtools (even though gmapR doesn't seem to use it internally).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@83106 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/11/2013 22:07:43
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... ...
@@ -10,10 +10,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.2
13
+Version: 1.5.3
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15
-Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
-         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
15
+Imports: IRanges, Rsamtools (>= 1.7.4), GenomicAlignments,
16
+         rtracklayer (>= 1.17.15), GenomicFeatures,
17
+         Biostrings, VariantAnnotation (>= 1.9.4), tools,
17 18
          Biobase, BSgenome
18 19
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 20
 	  BSgenome.Scerevisiae.UCSC.sacCer3,
Browse code

fix off-by-one in insertion positions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@82225 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2013 21:27:27
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.1
13
+Version: 1.5.2
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
Browse code

bam_tally annotates columns with Description field for inclusion in VCF header

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@82008 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 22/10/2013 22:49:06
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@@ -10,13 +10,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.5.0
13
+Version: 1.5.1
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15
-Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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-         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
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-         Biobase, BSgenome, methods
15
+Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
16
+         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,
17
+         Biobase, BSgenome
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19
-	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,
19
+	  BSgenome.Scerevisiae.UCSC.sacCer3,
20 20
           org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
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           BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
22 22
 License: Artistic-2.0
Browse code

bump version after release branch has been created

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@81644 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:47:19
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.4.0
13
+Version: 1.5.0
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

bump versions prior to creating BioC 2.13 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@81642 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:29:21
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.10
13
+Version: 1.4.0
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80611 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 20/09/2013 02:05:42
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.9
13
+Version: 1.3.10
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

support circular flag in seqinfo,GmapGenome

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80504 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 16/09/2013 23:22:09
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.8
13
+Version: 1.3.9
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

version bump, 1.3.8

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80235 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 10/09/2013 21:52:34
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.7
13
+Version: 1.3.8
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

try again to fix the gmap-mode argument handling

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80177 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 09/09/2013 23:12:49
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.6
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+Version: 1.3.7
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

fix default (NULL) for gmap-mode argument to gsnap

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80175 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 09/09/2013 21:59:47
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.5
13
+Version: 1.3.6
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

fix normalization of multi-base deletion sequences

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80139 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/09/2013 21:00:55
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.4
13
+Version: 1.3.5
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 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@79212 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2013 20:06:21
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.3
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+Version: 1.3.4
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78531 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 15/07/2013 23:44:31
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.2
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+Version: 1.3.3
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
16 16
          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
Browse code

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78427 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/07/2013 00:43:43
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@@ -13,8 +13,8 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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 Version: 1.3.2
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 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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-         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.17), tools,
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-         Biobase, BSgenome
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+         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.34), tools,
17
+         Biobase, BSgenome, methods
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 19
 	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,
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           org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
Browse code

package created by makeGmapGenomePackage now have a GmapGenome with the correct name

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@76649 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 16/05/2013 00:38:54
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@@ -10,11 +10,11 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.1
13
+Version: 1.3.2
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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-         GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase,
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-         BSgenome
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+         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.7.17), tools,
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+         Biobase, BSgenome
18 18
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
19 19
 	  BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,
20 20
           org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
Browse code

Use readDNAStringSet() instead of read.DNAStringSet().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@76521 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/05/2013 23:23:36
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.3.0
13
+Version: 1.3.1
14 14
 Depends: R (>= 2.15.0), methods, GenomicRanges
15 15
 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase,
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@@ -45,4 +45,4 @@ Collate: GmapBamReader-class.R
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          TP53Genome.R
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          utils.R
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 	 asSystemCall.R
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-         
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\ No newline at end of file
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+         
Browse code

Bump y in version x.y.z to odd number in devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75270 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 22:06:11
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
13
-Version: 1.2.0
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+Version: 1.3.0
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 Depends: R (>= 2.15.0), methods, GenomicRanges
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 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase,
Browse code

bump y of x.y.z version number for BioC 2.12 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75263 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 21:32:27
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11 11
     methods to tally alignment results on a per-nucleotide basis using 
12 12
     the bam_tally tool.
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-Version: 1.1.17
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+Version: 1.2.0
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 Depends: R (>= 2.15.0), methods, GenomicRanges
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 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,
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          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase,
Browse code

Make sure that the genome index exists before attempting to retrieve sequence.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75244 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 03/04/2013 18:46:36
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
10 10
     to work with GMAP and GSNAP from within R. In addition, it provides 
11