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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/samtools">Debian Med / samtools</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/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd">619dfea0</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-02-14T13:21:56+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapted patches, mahem patch was applied upstream
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<h4>4 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="#7689488b0611809fd3cf1973798c485006db95fe">
<span class="deleted-file">
−
debian/patches/mayhem.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="#1a48ab55cdba02e81517c3347c3e68888e1d1875">
debian/patches/sort-tests-memory-limit.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">samtools (1.7-1) 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"> * New upstream version</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> TODO: Adpapt patches</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version (adapted patches, mahem patch was applied upstream)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.1.3</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 14 Feb 2018 09:50:58 +0100</span>
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<li id="7689488b0611809fd3cf1973798c485006db95fe">
<a href="https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd#7689488b0611809fd3cf1973798c485006db95fe"><strong>debian/patches/mayhem.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Mon, 21 Dec 2015 13:20:46 +0100</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/716197</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> https://bugs.debian.org/716199</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Description: Fix Mayhem issues caused by unlimited reads of gz input</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Forwarded: https://github.com/samtools/samtools/issues/751</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Comment: Applied upstream</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> https://github.com/samtools/samtools/commit/10cc08958bcbbd47d2c3deb81881fcb12ec3a71e</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/misc/maq2sam.c</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/misc/maq2sam.c</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -99,14 +99,37 @@ maqmap_t *maqmap_read_header(gzFile fp)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> assert(mm->format == MAQMAP_FORMAT_NEW);</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> }</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gzread(fp, &mm->n_ref, sizeof(int));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( gzread(fp, &mm->n_ref, sizeof(int)) < sizeof(int)) {</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "To few bytes in input file");</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (mm->n_ref < 0) {</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Incorrect n_ref read from input file\n");</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( gzeof(fp) ) {</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Unexpected end of file.");</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></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;">+ }</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> for (k = 0; k != mm->n_ref; ++k) {</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( gzeof(fp) ) {</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;">+ fprintf(stderr, "Unexpected end of file.");</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</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"> gzread(fp, &len, sizeof(int));</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> mm->ref_name[k] = (char*)malloc(len * sizeof(char));</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;">+ if ( gzeof(fp) ) {</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;">+ fprintf(stderr, "Unexpected end of file.");</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;">+ return NULL;</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;">+ }</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> gzread(fp, mm->ref_name[k], len);</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> /* read number of mapped reads */</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;">+ if ( gzeof(fp) ) {</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Unexpected end of file.");</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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="LC48" class="line" lang="diff"> gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> return mm;</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,6 +141,8 @@ void maq2tam_core(gzFile fp, const char</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> int ret;</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> m1 = &mm1;</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> mm = maqmap_read_header(fp);</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (!mm) exit(1);</span></span>
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<pre style="margin: 0;">-<span id="LC56" 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="LC57" class="line" lang="diff"> while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> if (m1->flag) flag |= 1;</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -192,6 +217,11 @@ int main(int argc, char *argv[])</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> return 1;</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (!fp ) {</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Unable to open file %s", argv[1]);</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> maq2tam_core(fp, argc > 2? argv[2] : 0);</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> gzclose(fp);</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> return 0;</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">mayhem.patch</span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">sort-tests-memory-limit.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd#1a48ab55cdba02e81517c3347c3e68888e1d1875"><strong>debian/patches/sort-tests-memory-limit.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">@@ -6,7 +6,7 @@ Last-Update: 2017-12-22</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test.pl</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test.pl</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24<span class="idiff left right">65,22 +2465,22 @@</span></span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24<span class="idiff left right">72,22 +2472,22 @@ sub test_sort</span></span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> # Pos sort</span>
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