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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/fastqc">Debian Med / fastqc</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/82509227778c57e32e35d6c367063890ba309137">82509227</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-05-21T20:00:58Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix debian/patches/htsjdk-api.patch
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<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/bfda1c90add9818e96ed1d0686d3c64060fa09dc">bfda1c90</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-05-21T20:19:32Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/changelog
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#63dea3c1b316e739942b6628858062aaf9272421">
debian/patches/htsjdk-api.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Jelmer Vernooij ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Use secure copyright file specification URI.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +9,11 @@ fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * debian/fastqc.desktop: Update path to the icon.</span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Jelmer Vernooij <jelmer@debian.org> Sat, 20 Oct 2018 20:48:12 +0000</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [ Dylan Aïssi ]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Update d/patches/htsjdk-api.patch to fix processing</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> of SAM/BAM files (Closes: #897109). Thanks to Chris Norman.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Tue, 21 May 2019 22:16:30 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">fastqc (0.11.8+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<li id="63dea3c1b316e739942b6628858062aaf9272421">
<a href="https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc#63dea3c1b316e739942b6628858062aaf9272421"><strong>debian/patches/htsjdk-api.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ Description: use correct SamReader API</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Sascha Steinbiss <satta@debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -27,7 +27,9 @@<span class="idiff left right"> import java.util.List;</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -27,7 +27,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> import htsjdk.samtools.CigarElement;</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> import htsjdk.samtools.CigarOperator;</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> import htsjdk.samtools.SAMFormatException;</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> import htsjdk.samtools.SAMRecord;</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> import htsjdk.samtools.ValidationStringency;</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -44,7 +46,7 @@<span class="idiff left right"> public class BAMFile implements Sequence</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -44,7 +46,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> // only way to access the file pointer.</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> private FileInputStream fis;</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,22 +22,24 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> private String name;</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> private Sequence nextSequence = null;</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> Iterator<SAMRecord> it;</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -56,11 +58,1<span class="idiff left right">0 @@ public class BAMFile implements Sequence</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -56,11 +58,1<span class="idiff left right">2 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> name = file.getName();</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> this.onlyMapped = onlyMapped;</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SamInputResource sir = SamInputResource.of(fis);</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fis = new FileInputStream(file);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> fis = new FileInputStream(file);</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- br = new SAMFileReader(fis);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SamInputResource sir = SamInputResource.of(fis);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ br = srf.open(sir);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> it = br.iterator();</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> readNext();</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -135,7 +13<span class="idiff left right">6,7 @@ public class BAMFile implements Sequence</span></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -135,7 +13<span class="idiff left right">8,7 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> // through the file.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> if (recordSize == 0) {</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> recordSize = (record.getReadLength()*2)+150;</span>
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