Dylan Aïssi pushed to branch master at Debian Med / fastqc
Commits: 82509227 by Dylan Aïssi at 2019-05-21T20:00:58Z Fix debian/patches/htsjdk-api.patch - - - - - bfda1c90 by Dylan Aïssi at 2019-05-21T20:19:32Z Update d/changelog - - - - - 2 changed files: - debian/changelog - debian/patches/htsjdk-api.patch Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,7 @@ fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium + * Team upload. + [ Jelmer Vernooij ] * Trim trailing whitespace. * Use secure copyright file specification URI. @@ -7,7 +9,11 @@ fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium [ Michael R. Crusoe ] * debian/fastqc.desktop: Update path to the icon. - -- Jelmer Vernooij <[email protected]> Sat, 20 Oct 2018 20:48:12 +0000 + [ Dylan Aïssi ] + * Update d/patches/htsjdk-api.patch to fix processing + of SAM/BAM files (Closes: #897109). Thanks to Chris Norman. + + -- Dylan Aïssi <[email protected]> Tue, 21 May 2019 22:16:30 +0200 fastqc (0.11.8+dfsg-1) unstable; urgency=medium ===================================== debian/patches/htsjdk-api.patch ===================================== @@ -2,7 +2,7 @@ Description: use correct SamReader API Author: Sascha Steinbiss <[email protected]> --- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java +++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java -@@ -27,7 +27,9 @@ import java.util.List; +@@ -27,7 +27,9 @@ import htsjdk.samtools.CigarElement; import htsjdk.samtools.CigarOperator; @@ -13,7 +13,7 @@ Author: Sascha Steinbiss <[email protected]> import htsjdk.samtools.SAMFormatException; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.ValidationStringency; -@@ -44,7 +46,7 @@ public class BAMFile implements Sequence +@@ -44,7 +46,7 @@ // only way to access the file pointer. private FileInputStream fis; @@ -22,22 +22,24 @@ Author: Sascha Steinbiss <[email protected]> private String name; private Sequence nextSequence = null; Iterator<SAMRecord> it; -@@ -56,11 +58,10 @@ public class BAMFile implements Sequence +@@ -56,11 +58,12 @@ name = file.getName(); this.onlyMapped = onlyMapped; - SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT); -+ SamInputResource sir = SamInputResource.of(fis); -+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); - -- fis = new FileInputStream(file); +- + fis = new FileInputStream(file); - - br = new SAMFileReader(fis); ++ ++ SamInputResource sir = SamInputResource.of(fis); ++ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); ++ + br = srf.open(sir); it = br.iterator(); readNext(); -@@ -135,7 +136,7 @@ public class BAMFile implements Sequence +@@ -135,7 +138,7 @@ // through the file. if (recordSize == 0) { recordSize = (record.getReadLength()*2)+150; View it on GitLab: https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc -- View it on GitLab: https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc You're receiving this email because of your account on salsa.debian.org.
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