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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libucsc">Debian Med / libucsc</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/libucsc/commit/f6cc218e9af7e655959bea16a2c80067f806267e">f6cc218e</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-01-27T08:35:53+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use official htslib in libucsc
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<h4>2 changed files:</h4>
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#434539ac8d6610a4b8da3f69651325e8bcaaf68f">
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+
debian/patches/unbundle-htslib.patch
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<h4>Changes:</h4>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f6cc218e9af7e655959bea16a2c80067f806267e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># use_debian_packaged_htslib.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">unbundle-htslib.patch</span></pre>
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<li id="434539ac8d6610a4b8da3f69651325e8bcaaf68f">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f6cc218e9af7e655959bea16a2c80067f806267e#434539ac8d6610a4b8da3f69651325e8bcaaf68f"><strong>debian/patches/unbundle-htslib.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: John Marshall <John.W.Marshall@glasgow.ac.uk></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri Jan 24 14:34:54 GMT 2020</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use official htslib in libucsc</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Origin: https://alioth-lists.debian.net/pipermail/debian-med-packaging/2020-January/077104.html</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/lib/bamFile.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/lib/bamFile.c</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -7,10 +7,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #include "portable.h"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #include "bamFile.h"</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #include "htmshell.h"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "cram/cram_samtools.h"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "cram/sam_header.h"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "cram/cram_structs.h"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "htslib/cram.h"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "htslib/sam.h"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #include "udc.h"</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #include "psl.h"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -179,44 +176,6 @@</span> if (iter == NULL)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> int result;</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> while ((result = sam_itr_next(samfile, iter, b)) >= 0) </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> callbackFunc(b, callbackData, header);</span>
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<pre style="margin: 0;">+<span id="LC24" 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="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// if we're reading a CRAM file and the MD5 string has been set</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// we know there was an error finding the reference and we need</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// to request that it be loaded.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if (samfile->format.format == cram) </span></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;">- {</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;">- char *md5String = cram_get_Md5(samfile);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (!isEmpty(md5String))</span></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;">- char server[4096];</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char pendingFile[4096];</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char errorFile[4096];</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char *refPath = cram_get_ref_url(samfile);</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char *cacheDir = cram_get_cache_dir(samfile);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(server, refPath, md5String);</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(pendingFile, "%s/pending/",cacheDir);</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(errorFile, "%s/error/%s",cacheDir,md5String);</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- makeDirsOnPath(pendingFile);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(pendingFile, "%s/pending/%s",cacheDir,md5String);</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- FILE *downFile;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((downFile = fopen(errorFile, "r")) != NULL)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char errorBuf[4096];</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mustGetLine(downFile, errorBuf, sizeof errorBuf);</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- errAbort("cannot find reference %s. Error: %s\n", md5String,errorBuf);</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((downFile = fopen(pendingFile, "w")) == NULL)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- errAbort("cannot find reference %s. Cannot create file %s.",md5String, pendingFile); </span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(downFile, "%s\n", server);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fclose(downFile);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- errAbort("Cannot find reference %s. Downloading from %s. Please refresh screen to check download status.",md5String, server);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> }</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> void bamAndIndexFetchPlus(char *fileOrUrl, char *baiFileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -231,12 +190,6 @@</span> void bamAndIndexFetchPlus(char *fileOrUr</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> {</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> char *bamFileName = NULL;</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> samfile_t *fh = bamOpen(fileOrUrl, &bamFileName);</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if (fh->format.format == cram) </span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (cacheDir == NULL)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- errAbort("CRAM cache dir hg.conf variable (cramRef) must exist for CRAM support");</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cram_set_cache_url(fh, cacheDir, refUrl); </span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" 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="LC75" class="line" lang="diff"> bam_hdr_t *header = sam_hdr_read(fh);</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> if (pSamFile != NULL)</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> *pSamFile = fh;</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -256,16 +209,9 @@</span> static int bamGetTargetCount(char *fileO</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> {</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> int tCount = 0;</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> htsFile *htsF = hts_open(fileOrUrl, "r");</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if (htsF->format.format == crai)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAM_hdr *cramHdr = cram_fd_get_header(htsF->fp.cram);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tCount = cramHdr->nref;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bam_hdr_t *bamHdr = bam_hdr_read(htsF->fp.bgzf);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tCount = bamHdr->n_targets;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bam_hdr_t *bamHdr = sam_hdr_read(htsF);</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tCount = bamHdr->n_targets;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bam_hdr_destroy(bamHdr);</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> hts_close(htsF);</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> return tCount;</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> }</span></pre>
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