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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/vt">Debian Med / vt</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/vt/-/commit/4df59f7e5ea792d4e13e442d265251c7a10ab177">4df59f7e</a></strong>
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<span>by Antoni Villalonga</span>
<i>at 2020-11-09T07:47:35+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch 0001: Get rid of commented code
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<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/c9a3a2be69f779509142f49346a01d16dea93f75">c9a3a2be</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-09T08:02:03+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'patch-0001-amend' into 'master'
patch 0001: Get rid of commented code
See merge request med-team/vt!1</pre>
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<h4>1 changed file:</h4>
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<a href="#c0f5aeb1d873bb3881f1f49eb99b8ef890746c60">
debian/patches/0001-updated-faidx_fetch_uc_seq.patch
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<h4>Changes:</h4>
<li id="c0f5aeb1d873bb3881f1f49eb99b8ef890746c60">
<a href="https://salsa.debian.org/med-team/vt/-/compare/73a50b1d13545bdf058829a7159ae720c8131407...c9a3a2be69f779509142f49346a01d16dea93f75#c0f5aeb1d873bb3881f1f49eb99b8ef890746c60"><strong>debian/patches/0001-updated-faidx_fetch_uc_seq.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">@@ -3,11 +3,9 @@ From: Adrian Tan <atks@umich.edu></td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Date: Fri, 13 Jul 2018 17:20:56 -0400</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Subject: updated faidx_fetch_uc_seq</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">diff --git a/hts_utils.cpp b/hts_utils.cpp</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">index 6644f0e..30bf37a 100644</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/hts_utils.cpp</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/hts_utils.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -40,3<span class="idiff left">7 +40,53 @@</span></span><span class="idiff right"> typedef khash_t(vdict) vdict_t;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -40,3<span class="idiff left right">6 +40,14 @@</span></span></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"> char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)</span>
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<pre style="margin: 0;"> <span id="LC11" 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">@@ -30,65 +28,23 @@ index 6644f0e..30bf37a 100644</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // Now retrieve the sequence</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;">- int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);</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;">- if ( ret<0 )</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;">- {</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;">+ char* seq = faidx_fetch_seq(fai, c_name, p_beg_i, p_end_i, len);</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;">+ </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;">+ </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;">+ for (int32_t i=0; i<*len; ++i)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *len = -1;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC37" 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="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (isgraph(seq[i])) seq[i] = toupper(seq[i]);</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = 0;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq = (char*)malloc(p_end_i - p_beg_i + 2);</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)</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;">- if (isgraph(c)) seq[l++] = toupper(c);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq[l] = '\0';</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *len = l;</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;">+ char* seq = faidx_fetch_seq(fai, c_name, p_beg_i, p_end_i, len);</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;">+ </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;">+ </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;">+ // while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if (isgraph(c)) seq[l++] = toupper(c);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// seq[l] = '\0';</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// *len = l;</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (int32_t i=0; i<*len; ++i)</span></span>
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<pre style="margin: 0;">-<span id="LC53" 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="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (isgraph(seq[i])) seq[i] = toupper(seq[i]);</span></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;">+ }</span></span>
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47
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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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57
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> return seq;</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// int l;</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// char c;</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// khiter_t iter;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// faidx1_t val;</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// char *seq=NULL;</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // Adjust position</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// iter = kh_get(s, fai->hash, c_name);</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if(iter == kh_end(fai->hash)) return 0;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// val = kh_value(fai->hash, iter);</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if(p_end_i < p_beg_i) p_beg_i = p_end_i;</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if(p_beg_i < 0) p_beg_i = 0;</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// else if(val.len <= p_beg_i) p_beg_i = val.len - 1;</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if(p_end_i < 0) p_end_i = 0;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// else if(val.len <= p_end_i) p_end_i = val.len - 1;</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// // Now retrieve the sequence</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if ( ret<0 )</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" 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="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// *len = -1;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// return NULL;</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// }</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// l = 0;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// seq = (char*)malloc(p_end_i - p_beg_i + 2);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// if (isgraph(c)) seq[l++] = toupper(c);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// seq[l] = '\0';</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// *len = l;</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// return seq;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"> /**********</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"></span></pre>
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