1. ShortRead
  2. DESCRIPTION
Browse code

avoid integer overflow in countFastq

- closes #10

Martin Morgan authored on 16/11/2022 12:57:29
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.57.0
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+Version: 1.57.1
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 Authors@R: c(
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         person("Bioconductor Package", "Maintainer",  role="cre",
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             email="maintainer@bioconductor.org"),
Browse code

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

J Wokaty authored on 01/11/2022 15:03:51
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.56.0
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+Version: 1.57.0
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 Authors@R: c(
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         person("Bioconductor Package", "Maintainer",  role="cre",
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             email="maintainer@bioconductor.org"),
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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 15:03:51
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DESCRIPTION
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1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.55.2
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+Version: 1.56.0
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 Authors@R: c(
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         person("Bioconductor Package", "Maintainer",  role="cre",
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             email="maintainer@bioconductor.org"),
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version bump

Martin Morgan authored on 20/10/2022 20:13:59
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DESCRIPTION
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1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.55.1
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+Version: 1.55.2
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 Authors@R: c(
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         person("Bioconductor Package", "Maintainer",  role="cre",
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             email="maintainer@bioconductor.org"),
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add URL: and BugReports:, use Authors@R in DESCRIPTION

- closes #6

Martin Morgan authored on 16/10/2022 19:10:17
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DESCRIPTION
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1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
4 
-Version: 1.55.0
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-Author: Martin Morgan, Michael Lawrence, Simon Anders
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-Maintainer: Bioconductor Package Maintainer
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-        <maintainer@bioconductor.org>
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+Version: 1.55.1
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+Authors@R: c(
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+        person("Bioconductor Package", "Maintainer",  role="cre",
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+            email="maintainer@bioconductor.org"),
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+        person("Martin", "Morgan", role = "aut"),
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+        person("Michael", "Lawrence", role = "ctb"),
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+        person("Simon", "Anders", role = "ctb")
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+    )
8 12 
 Description: This package implements sampling, iteration, and input of
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         FASTQ files. The package includes functions for filtering and
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         trimming reads, and for generating a quality assessment report.
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@@ -22,3 +26,7 @@ Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
22 26 
 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
23 27 
 LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
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 biocViews: DataImport, Sequencing, QualityControl
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+URL: https://bioconductor.org/packages/ShortRead,
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+    https://github.com/Bioconductor/ShortRead,
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+    https://support.bioconductor.org/tag/ShortRead
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+BugReports: https://github.com/Bioconductor/ShortRead/issues
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:01:12
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DESCRIPTION
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1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.54.0
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+Version: 1.55.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:01:12
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DESCRIPTION
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 Package: ShortRead
2 2 
 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.53.1
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+Version: 1.54.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
Browse code

Get ShortRead ready for the switch to virtual DataFrame (in S4Vectors package)

Hervé Pagès authored on 16/11/2021 06:01:25
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DESCRIPTION
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 Package: ShortRead
2 2 
 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.53.0
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+Version: 1.53.1
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:52:20
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.52.0
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+Version: 1.53.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:52:20
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.51.0
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+Version: 1.52.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:40:52
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.50.0
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+Version: 1.51.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:40:52
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DESCRIPTION
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 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.49.3
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+Version: 1.50.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
Browse code

don't segfault on re-serialized FastqStreamer / FastqSampler

- closes #5

Martin Morgan authored on 17/05/2021 09:49:19
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.49.2
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+Version: 1.49.3
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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no more hot fix

Hervé Pagès authored on 03/02/2021 19:10:45
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.49.1
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+Version: 1.49.2
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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version bump

- ee71f25 and adf4a49 closes #3

Martin Morgan authored on 10/12/2020 20:19:31
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History View file @ e2eb649
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.49.0
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+Version: 1.49.1
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 14:33:27
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 Package: ShortRead
2 2 
 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.48.0
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+Version: 1.49.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 14:33:27
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.47.2
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+Version: 1.48.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
Browse code

missing header file for countFastq

Martin Morgan authored on 27/05/2020 09:24:05
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.47.1
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+Version: 1.47.2
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
Browse code

Merge remote-tracking branch 'refs/remotes/upstream/master'

Martin Morgan authored on 23/05/2020 21:40:33
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Browse code

add countFastq for fast counting of fastq records

Martin Morgan authored on 23/05/2020 21:27:06
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DESCRIPTION
History View file @ 2fc1782
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@@ -20,5 +20,5 @@ Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
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         GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8),
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         hwriter, methods, zlibbioc, lattice, latticeExtra,
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 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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-LinkingTo: S4Vectors, IRanges, XVector, Biostrings
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+LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
24 24 
 biocViews: DataImport, Sequencing, QualityControl
Browse code

Remove coercion from AlignedRead to RangedData

Hervé Pagès authored on 02/05/2020 06:54:36
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.47.0
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+Version: 1.47.1
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 18:17:12
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.46.0
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+Version: 1.47.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 18:17:12
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.45.4
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+Version: 1.46.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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version bump

Martin Morgan authored on 18/03/2020 20:03:16
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.45.3
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+Version: 1.45.4
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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Merge branch 'RELEASE_3_10'

- unit test update

Martin Morgan authored on 03/02/2020 20:40:50
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update unit test

- alias .qualityTypeAuto()

Martin Morgan authored on 03/02/2020 20:39:26
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DESCRIPTION
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.44.2
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+Version: 1.44.3
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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Merge branch 'RELEASE_3_10' -- readFastq qualityType = "Auto"

Martin Morgan authored on 30/01/2020 22:56:15
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readFastq argument qualityType = "Auto" detects SFastqQuality correctly

- closes #2

Martin Morgan authored on 30/01/2020 22:54:13
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DESCRIPTION
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 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.44.1
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+Version: 1.44.2
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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Merge branch 'RELEASE_3_10' (bugfix: internal: avoid lenght > 1 logical test)

Martin Morgan authored on 19/12/2019 16:53:21
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bugfix: internal: avoid length > 1 logical test

Martin Morgan authored on 19/12/2019 16:52:09
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DESCRIPTION
History View file @ a5041a8
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.44.0
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+Version: 1.44.1
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 17:34:49
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.44.0
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+Version: 1.45.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 17:07:56
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DESCRIPTION
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.43.2
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+Version: 1.44.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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Using Rs CFLAGS and LDFLAGS

Kasper Daniel Hansen authored on 09/09/2019 15:24:52
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DESCRIPTION
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 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.43.1
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+Version: 1.43.2
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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Use is(x, "DataFrame") instead of class(x) == "DataFrame"

Hervé Pagès authored on 17/08/2019 02:34:12
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History View file @ f95f223
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.43.0
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+Version: 1.43.1
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 16:10:47
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DESCRIPTION
History View file @ 3d4f5a4
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 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.42.0
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+Version: 1.43.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:53:10
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DESCRIPTION
History View file @ daa2576
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.41.0
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+Version: 1.42.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:54:27
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History View file @ b695537
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 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.40.0
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+Version: 1.41.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 15:41:44
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History View file @ 0cbe4b6
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.39.0
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+Version: 1.40.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 14:41:37
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DESCRIPTION
History View file @ 4525ba1
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 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.38.0
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+Version: 1.39.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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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 14:35:09
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DESCRIPTION
History View file @ e9498f0
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1 1 
 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.37.5
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+Version: 1.38.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
Browse code

Use get_List_elementType() instead of get_XStringSet_xsbaseclassname()

C function get_XStringSet_xsbaseclassname() defined in the Biostrings
package was just a wrapper around C function get_List_elementType()
defined in the S4Vectors package. This wrapper is not needed anymore
and is about to be removed from Biostrings.

Hervé Pagès authored on 16/03/2018 01:54:35
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History View file @ be12ac5
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1 1 
 Package: ShortRead
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 Type: Package
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 Title: FASTQ input and manipulation
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-Version: 1.37.4
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+Version: 1.37.5
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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change location of sread(), id() docs

- NOT 'legacy'

Martin Morgan authored on 06/03/2018 20:52:37
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DESCRIPTION
History View file @ 3a60b21
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1 1 
 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.37.3
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+Version: 1.37.4
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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version bump and NEWS entry

Martin Morgan authored on 21/02/2018 10:59:25
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DESCRIPTION
History View file @ eaec3c7
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1 1 
 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.37.2
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+Version: 1.37.3
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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FastqQuality should include '~'

- see https://support.bioconductor.org/p/106144/

Martin Morgan authored on 20/02/2018 22:17:06
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         <maintainer@bioconductor.org>
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follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:31:32
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-        2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
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+        2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
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+Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
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         hwriter, methods, zlibbioc, lattice, latticeExtra,
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 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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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 16:52:08
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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 16:39:23
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Apply "hotfix 73465" to FastqFileList(), FastqStreamerList(), and FastqSamplerList() generics (see file R/hotfix73465.R in package BiocGenerics for more information).

Hervé Pagès authored on 07/10/2017 02:12:10
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version bump

Martin Morgan authored on 30/08/2017 20:28:50
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use pruning.mode="coarse" instead of force=TRUE when calling seqlevels() setter

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@129294 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/04/2017 21:21:50
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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/ShortRead@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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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/ShortRead@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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some tweaks in reponse to latest changes in S4Vectors C interface

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@126085 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 23/01/2017 05:56:48
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 Depends: BiocGenerics (>= 0.11.3), BiocParallel, Biostrings (>=
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         2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
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-Imports: Biobase, S4Vectors (>= 0.7.1), IRanges (>= 2.3.7),
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         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6),
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         hwriter, methods, zlibbioc, lattice, latticeExtra,
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 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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/ShortRead@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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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/ShortRead@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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Need to define the left() and right() generics here now that they've been removed from GenomicAlignments.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@119243 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 10/07/2016 08:46:24
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bump version after creating 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:30:44
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Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
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typo in man page example

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@114812 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 15/03/2016 21:59:45
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Browse code

cleanup: rename readInfo as readIntensityInfo

- part of 'legacy' code
- avoids conflict with VariantAnnotation::readInfo


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@114694 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 13/03/2016 12:15:11
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bugfix: resolve malloc & friends to std:: namespace in C++ code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@114540 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 09/03/2016 16:52:54
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cleanup: lengths() instead of elementLengths()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@112827 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 23/01/2016 17:31:44
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Browse code

unname colClasses in read.table

- probably a bug introduced into R-devel


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@109902 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 25/10/2015 06:13:12
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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/ShortRead@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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Bumped versions of all packages prior to creating 3.2 branch.

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

Dan Tenenbaum authored on 13/10/2015 19:36:05
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Browse code

implement [<,ShortReadQ-method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@105724 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 01/07/2015 13:08:43
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Browse code

vignette typo (from Jonathan van Eyll)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@103917 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/05/2015 11:50:46
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missing(...) replaces length(list(...)) == 0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@103387 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 02/05/2015 22:10:24
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resync with major refactoring of C-level Auto-Extending buffers in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@103289 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 30/04/2015 00:03:48
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-        2.33.14), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.28)
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 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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Browse code

unnecessary Suggests: removed

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@102917 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 21/04/2015 23:53:28
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 biocViews: DataImport, Sequencing, QualityControl
Browse code

update NEWS and version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@102916 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 21/04/2015 23:51:47
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@@ -19,6 +19,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocParallel, Biostrings (>=
19 19 
 Imports: Biobase, S4Vectors (>= 0.5.11), IRanges (>= 1.99.27),
20 20 
         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.17.39),
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         hwriter, methods, zlibbioc, lattice, latticeExtra,
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-Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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+Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, GenomicFiles,
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+        yeastNagalakshmi
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 LinkingTo: S4Vectors, IRanges, XVector, Biostrings
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 biocViews: DataImport, Sequencing, QualityControl
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Bump versions in trunk after creation of 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 20:02:44
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 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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-Version: 1.26.0
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+Version: 1.27.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
6 6 
 Maintainer: Bioconductor Package Maintainer
7 7 
         <maintainer@bioconductor.org>
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Bump versions prior to creating 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 19:42:01
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1 1 
 Package: ShortRead
2 2 
 Type: Package
3 3 
 Title: FASTQ input and manipulation
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+Version: 1.26.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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mark readAligned for BAM files as deprecated

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@101602 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 30/03/2015 17:47:19
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1 1 
 Package: ShortRead
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 Title: FASTQ input and manipulation
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-Version: 1.25.9
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+Version: 1.25.10
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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         <maintainer@bioconductor.org>
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install C symbols to avoid protection stack imbalance

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@100365 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/03/2015 12:06:04
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1 1 
 Package: ShortRead
2 2 
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 Title: FASTQ input and manipulation
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-Version: 1.25.8
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         <maintainer@bioconductor.org>
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writeFastq,*,FastqFile-method mode and compress bug fixes

- obey 'compress' argument
- require 'mode'


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@97376 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 04/12/2014 16:18:37
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 Package: ShortRead
2 2 
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-Version: 1.25.7
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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         <maintainer@bioconductor.org>
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'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and Doubles_holder.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@97100 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 25/11/2014 10:37:15
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1 1 
 Package: ShortRead
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-Version: 1.25.6
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@@ -16,7 +16,7 @@ License: Artistic-2.0
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 LazyLoad: yes
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 Depends: BiocGenerics (>= 0.11.3), BiocParallel, Biostrings (>=
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         2.33.14), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.28)
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-Imports: Biobase, S4Vectors (>= 0.2.2), IRanges (>= 1.99.27),
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+Imports: Biobase, S4Vectors (>= 0.5.11), IRanges (>= 1.99.27),
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         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.17.39),
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         hwriter, methods, zlibbioc, lattice, latticeExtra,
22 22 
 Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
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document use of OpenMP in FastqStreamer / Sampler and trim*

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96860 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/11/2014 18:51:39
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-Version: 1.25.5
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+Version: 1.25.6
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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further PROTECTs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96750 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 14/11/2014 05:38:58
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-Version: 1.25.4
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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PROTECT lang1(), lang2() return values before evaluating

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96706 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 13/11/2014 02:10:56
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-Version: 1.25.3
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+Version: 1.25.4
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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close opened files when parsing old formats

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96702 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 12/11/2014 21:58:49
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-Version: 1.25.2
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+Version: 1.25.3
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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         <maintainer@bioconductor.org>
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Bump version to force replacement of stalled ShortRead.so file on the user machine. Details: the C API has changed in S4Vectors 0.5.4 and IRanges 2.1.6 so ShortRead.so will become stalled when the user installs these new versions of S4Vectors and IRanges.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96500 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/11/2014 07:07:22
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-Version: 1.25.1
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+Version: 1.25.2
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         <maintainer@bioconductor.org>
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version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@96295 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 31/10/2014 19:01:47
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 Title: FASTQ input and manipulation
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         <maintainer@bioconductor.org>
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Bumping versions after creating 3.0 release branch.

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

Dan Tenenbaum authored on 13/10/2014 21:47:41
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-Version: 1.24.0
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+Version: 1.25.0
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 Maintainer: Bioconductor Package Maintainer
7 7 
         <maintainer@bioconductor.org>
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Bump package versions prior to creating the 3.0 branch.

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

Dan Tenenbaum authored on 13/10/2014 21:38:33
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-Version: 1.23.17
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+Version: 1.24.0
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 Author: Martin Morgan, Michael Lawrence, Simon Anders
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 Maintainer: Bioconductor Package Maintainer
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         <maintainer@bioconductor.org>
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qa(..., sample=FALSE) no longer re-matches 'pattern'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@94240 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/09/2014 17:46:50
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-Version: 1.23.16
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+Version: 1.23.17
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         <maintainer@bioconductor.org>
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qa[["adapterContamination"]] should be real, not factor / character

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@94044 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 11/09/2014 21:24:31
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