1. gmapR
  2. DESCRIPTION
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ fea773c
... ... 
@@ -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: 1.40.0
12 
+Version: 1.41.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ ba9a187
... ... 
@@ -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
12 
+Version: 1.40.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 40d4db9
... ... 
@@ -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: 1.38.0
12 
+Version: 1.39.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ f762532
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 4fda1cc
... ... 
@@ -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
12 
+Version: 1.37.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 1e9cf9a
... ... 
@@ -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
12 
+Version: 1.36.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 43bb861
... ... 
@@ -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
12 
+Version: 1.35.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 3262a4e
... ... 
@@ -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
12 
+Version: 1.34.0
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),
Browse code

simplify email address

Michael Lawrence authored on 05/01/2021 19:14:02
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DESCRIPTION
History View file @ 38f36e1
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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
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ a7bc7ca
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 47ad3c2
... ... 
@@ -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
12 
+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)
15 15 
 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ c754fa3
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 08251b2
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ b5039ae
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 70a270e
... ... 
@@ -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
12 
+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),
Browse code

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
Showing 1 changed files
DESCRIPTION
History View file @ c3db7e3
... ... 
@@ -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
12 
+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),
Browse code

update GSTRUCT source code

Michael Lawrence authored on 22/05/2019 19:39:45
Showing 1 changed files
DESCRIPTION
History View file @ 7cb8750
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 095eb21
... ... 
@@ -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
12 
+Version: 1.27.0
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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 95ed5f3
... ... 
@@ -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
12 
+Version: 1.26.0
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),
Browse code

embed samtools sources directly, since Rsamtools has moved to htslib

Michael Lawrence authored on 11/02/2019 20:33:07
Showing 1 changed files
DESCRIPTION
History View file @ 5bb21ad
... ... 
@@ -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: 1.25.2
12 
+Version: 1.25.3
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),
Browse code

bam tally no longer crashes when NM exceeds maximum bin

Michael Lawrence authored on 05/02/2019 19:11:42
Showing 1 changed files
DESCRIPTION
History View file @ 3c11255
... ... 
@@ -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
12 
+Version: 1.25.2
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),
Browse code

version bump

Michael Lawrence authored on 20/11/2018 19:02:28
Showing 1 changed files
DESCRIPTION
History View file @ 9cc44e8
... ... 
@@ -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
12 
+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),
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:30
Showing 1 changed files
DESCRIPTION
History View file @ 922ee59
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ 19a2eb1
... ... 
@@ -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
12 
+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),
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:49:42
Showing 1 changed files
DESCRIPTION
History View file @ 4aae21b
... ... 
@@ -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
12 
+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),
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:39
Showing 1 changed files
DESCRIPTION
History View file @ cda7c25
... ... 
@@ -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
12 
+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),
Browse code

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
Showing 1 changed files
DESCRIPTION
History View file @ e2621b2
... ... 
@@ -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
12 
+Version: 1.22.0
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),
Browse code

follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:24:43
Showing 1 changed files
DESCRIPTION
History View file @ c087114
... ... 
@@ -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
12 
+Version: 1.21.3
13 13 
 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
14 
-        GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
15 
-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
14 
+        GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
15 
+Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
16 
+        rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings,
17 
+        VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome,
18 
+        GenomicAlignments (>= 1.15.6), 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

The path() generic has moved from Rsamtools to BiocGenerics

LiNk-NY authored on 20/12/2017 20:04:28
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DESCRIPTION
History View file @ c67b519
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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
12 
+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,
18 18 
         GenomicAlignments (>= 1.1.9), BiocParallel
Browse code

version bump

Michael Lawrence authored on 14/11/2017 23:02:49
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DESCRIPTION
History View file @ 99ba020
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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: 1.21.0
12 
+Version: 1.21.1
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 (>= 0.13.13), 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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DESCRIPTION
History View file @ 433a26b
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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
12 
+Version: 1.21.0
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 even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:47
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DESCRIPTION
History View file @ e20d214
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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
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

fixes for keep_ref=TRUE

Michael Lawrence authored on 14/09/2017 18:30:38
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DESCRIPTION
History View file @ 071760a
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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
12 
+Version: 1.19.2
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

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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DESCRIPTION
History View file @ 8ec8fe1
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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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DESCRIPTION
History View file @ 69da1e1
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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
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 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 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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DESCRIPTION
History View file @ 38b3975
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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
12 
+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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DESCRIPTION
History View file @ e1b17d3
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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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DESCRIPTION
History View file @ 32a9b51
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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
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         GmapParam-class.R GsnapParam-class.R
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         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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DESCRIPTION
History View file @ 55d77a1
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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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DESCRIPTION
History View file @ 28abe94
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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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DESCRIPTION
History View file @ e945492
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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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DESCRIPTION
History View file @ aba57c5
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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
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+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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DESCRIPTION
History View file @ 3748356
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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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DESCRIPTION
History View file @ 8b7fd7a
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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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DESCRIPTION
History View file @ c3d54b8
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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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DESCRIPTION
History View file @ 12074fe
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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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DESCRIPTION
History View file @ d92a799
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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),
14 14 
         GenomicRanges (>= 1.17.12)
15 
-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
16 
-        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
17 
-        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,
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,
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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DESCRIPTION
History View file @ d36ac68
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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
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+Version: 1.13.8
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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

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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DESCRIPTION
History View file @ cb7ab58
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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
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+Version: 1.13.7
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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

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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DESCRIPTION
History View file @ f053c5f
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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
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+Version: 1.13.6
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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 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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DESCRIPTION
History View file @ 5659f09
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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
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 (>= 1.31.2),
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
Showing 1 changed files
DESCRIPTION
History View file @ ead94b3
... ... 
@@ -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),
17 17 
         tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
18 18 
 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
... ... 
@@ -21,7 +21,9 @@ Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
21 21 
         LungCancerLines
22 22 
 Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
23 23 
         GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
24 
-        GsnapParam-class.R GsnapOutput-class.R atoiindex-command.R
24 
+        GmapParam-class.R GsnapParam-class.R
25 
+        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
Showing 1 changed files
DESCRIPTION
History View file @ 2332d26
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 685d60e
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 8418591
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 1f42582
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ e4a80ba
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 093e455
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 5be0f7d
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ f777bf1
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ d5ed124
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ c8fd96e
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ f58d4e9
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 81809a5
... ... 
@@ -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
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 768f7ee
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 438eb00
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ 74581e5
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ cfb01d1
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ c78be69
... ... 
@@ -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
Showing 1 changed files
DESCRIPTION
History View file @ c0cce6c
... ... 
@@ -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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DESCRIPTION
History View file @ f5e63d3
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@@ -10,7 +10,7 @@ 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,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.7.4
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+Version: 1.7.5
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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 (>= 1.25.5),
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
Showing 1 changed files
DESCRIPTION
History View file @ 9f0e3a7
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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,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.7.3
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+Version: 1.7.4
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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 (>= 1.25.5),
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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DESCRIPTION
History View file @ 6cca01e
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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
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         per-nucleotide basis using the bam_tally tool.
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 Version: 1.7.3
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-Depends: R (>= 2.15.0), methods, GenomicRanges
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-Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
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-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),
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-        tools, Biobase, BSgenome, GenomicAlignments
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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 (>= 1.25.5),
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+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.4),
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+        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9)
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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

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
Showing 1 changed files
DESCRIPTION
History View file @ 96cf993
... ... 
@@ -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.
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-Version: 1.7.2
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+Version: 1.7.3
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 Depends: R (>= 2.15.0), methods, GenomicRanges
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 Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
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         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
Showing 1 changed files
DESCRIPTION
History View file @ f7ab666
... ... 
@@ -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,
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         it provides methods to tally alignment results on a
12 12 
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.7.1
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+Version: 1.7.2
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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),
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-        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),
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+Imports: S4Vectors, IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
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+        GenomicFeatures, Biostrings, VariantAnnotation (>= 1.11.1),
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         tools, Biobase, BSgenome, GenomicAlignments
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 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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         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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DESCRIPTION
History View file @ 6a7e619
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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,
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         it provides methods to tally alignment results on a
12 12 
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.7.0
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+Version: 1.7.1
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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),
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         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
Showing 1 changed files
DESCRIPTION
History View file @ 73541fd
... ... 
@@ -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.
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-Version: 1.6.0
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+Version: 1.7.0
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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),
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         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
Showing 1 changed files
DESCRIPTION
History View file @ 63374d6
... ... 
@@ -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,
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         it provides methods to tally alignment results on a
12 12 
         per-nucleotide basis using the bam_tally tool.
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-Version: 1.5.15
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+Version: 1.6.0
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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),
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