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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f">972db398</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-07-04T16:51:45+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Helping compilation of sambamba
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#08203429b53d7fa2f4760940c31cbde4eb76e64b">
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+
debian/patches/cram_to_bam_export.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.10.2</span><span class="p">-</span><span class="m" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">d</span><span class="p">/</span><span class="n" style="color: #333;">control</span><span class="p">:</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">Rules</span><span class="p">-</span><span class="n" style="color: #333;">Requires</span><span class="p">-</span><span class="n" style="color: #333;">Root</span><span class="p">:</span> <span class="n" style="color: #333;">no</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Exported</span> <span class="n" style="color: #333;">cram_to_bam</span> <span class="k" style="font-weight: 600;">function</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">compile</span> <span class="n" style="color: #333;">sambamba</span><span class="p">,</span> <span class="n" style="color: #333;">borrowed</span> <span class="k" style="font-weight: 600;">from</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">git</span><span class="p">.</span><span class="n" style="color: #333;">genenetwork</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">guix</span><span class="p">-</span><span class="n" style="color: #333;">bioinformatics</span><span class="p">/</span><span class="n" style="color: #333;">guix</span><span class="p">-</span><span class="n" style="color: #333;">bioinformatics</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">htslib</span><span class="p">-</span><span class="n" style="color: #333;">add</span><span class="p">-</span><span class="n" style="color: #333;">cram_to_bam</span><span class="p">.</span><span class="n" style="color: #333;">patch</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">Moeller</span> <span class="p"><</span><span class="n" style="color: #333;">moeller</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Sat</span><span class="p">,</span> <span class="m" style="color: #099;">04</span> <span class="n" style="color: #333;">Jul</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">14</span><span class="p">:</span><span class="m" style="color: #099;">04</span><span class="p">:</span><span class="m" style="color: #099;">35</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.10.2</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p">]</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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 +2,8 @@ Source: htslib</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Charles Plessy <plessy@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Michael R. Crusoe <crusoe@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Michael R. Crusoe <crusoe@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Section: science</span>
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7
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<td class="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -17,6 +18,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/htslib</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/htslib.git</span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: https://github.com/samtools/htslib</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: libhts3</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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>
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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">@@ -60,6 +62,9 @@ Description: development files for the HTSlib</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> This package contains development files for the HTSlib: headers, static</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> library, manual pages, etc.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> For compatibility with sambamba, the internal routine cram_to_bam was</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> exported, hereto adopting a patch found in guix.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Package: htslib-test</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">Architecture: all</span>
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<li id="08203429b53d7fa2f4760940c31cbde4eb76e64b">
<a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f#08203429b53d7fa2f4760940c31cbde4eb76e64b"><strong>debian/patches/cram_to_bam_export.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Exports the cram_to_bam function to support the</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> sambamba package.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Roel Janssen <roel@gnu.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Index: htslib/cram/cram_decode.c</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- htslib.orig/cram/cram_decode.c</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ htslib/cram/cram_decode.c</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -2803,8 +2803,8 @@</span> int cram_decode_slice_mt(cram_fd *fd, cr</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> * Returns the used size of the bam record on success</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> * -1 on failure.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static int cram_to_bam(sam_hdr_t *sh, cram_fd *fd, cram_slice *s,</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cram_record *cr, int rec, bam_seq_t **bam) {</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int cram_to_bam(sam_hdr_t * const sh, const cram_fd * const fd, cram_slice * const s,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cram_record * const cr, int rec, bam_seq_t **bam) {</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> int bam_idx, rg_len;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> char name_a[1024], *name;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> int name_len;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">Index: htslib/cram/cram_decode.h</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- htslib.orig/cram/cram_decode.h</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ htslib/cram/cram_decode.h</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -106,6 +106,23 @@</span> int cram_decode_slice(cram_fd *fd, cram_</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Converts a cram in-memory record into a bam in-memory record. We</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * pass a pointer to a bam_seq_t pointer along with the a pointer to</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;">+ * the allocated size. These can initially be pointers to NULL and zero.</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;">+ *</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * This function will reallocate the bam buffer as required and update</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * (*bam)->alloc accordingly, allowing it to be used within a loop</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;">+ * efficiently without needing to allocate new bam objects over and</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;">+ * over again.</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Returns the used size of the bam record on success</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * -1 on failure.</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" 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="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+int cram_to_bam(SAM_hdr * const bfd, const cram_fd * const fd, cram_slice * const s,</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cram_record *const cr, int rec, bam_seq_t **bam);</span></span>
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<pre style="margin: 0;">+<span id="LC42" 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="LC43" 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="LC44" 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="LC45" class="line" lang="diff"> * Drains and frees the decode read-queue for a multi-threaded reader.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> void cram_drain_rqueue(cram_fd *fd);</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,3 +4,4 @@ fPIC.patch</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">testShebang.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix_float_precision</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">big-endian</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">cram_to_bam_export.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/-/commit/972db398ea64df81b6adc890a81c5506f33b3a7f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -54,6 +54,10 @@ override_dh_auto_install-arch:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> $(RM) -r test</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> mv test_backup test</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">override_dh_strip:</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> # This is apparently important for the interpretation by ldc2 in sambamba</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> dh_strip -Xlibhts.a</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">override_dh_auto_install-indep:</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>
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59
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">override_dh_auto_test-arch:</span>
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