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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libbigwig">Debian Med / libbigwig</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbigwig/commit/7755c72fcc610a874ea678d3ae85cc0c39875f8a">7755c72f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-05T11:34:45Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.4+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbigwig/commit/c41a87633c9cc5b699861162ee3312d084b2f807">c41a8763</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-05T11:51:02Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.4+dfsg</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9aab895775dcc7220eb583d52463759054d493e3">
bigWig.h
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<li class="file-stats">
<a href="#b4b53d426209550bb804b2936264ec0aa7750996">
bwRead.c
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<li class="file-stats">
<a href="#2da8b51e3330d487a1640608d75f54107f75cf32">
bwValues.c
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<li class="file-stats">
<a href="#0121f0e8888f2302c167fa994f3bfdff833daa69">
io.c
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -2,154 +2,160 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">A C library for reading/parsing local and remote bigWig and bigBed files. While Kent's source code is free to use for these purposes, it's really inappropriate as library code since it has the unfortunate habit of calling <span class="sb" style="color: #d14;">`exit()`</span> whenever there's an error. If that's then used inside of something like python then the python interpreter gets killed. This library is aimed at resolving these sorts of issues and should also use more standard things like curl and has a friendlier license to boot.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">Documentation is automatically generated by doxygen and can be found under <span class="sb" style="color: #d14;"><span class="idiff left right">`docs/html`</span></span> or online <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cdn.rawgit.com/dpryan79/libBigWig/master/docs/html/index.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">Documentation is automatically generated by doxygen and can be found under <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">`docs/html`</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">/docs/html</span></span><span class="p"><span class="idiff right">)</span></span> or online <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://cdn.rawgit.com/dpryan79/libBigWig/master/docs/html/index.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gh" style="color: #999;"># Example</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">The only functions and structures that end users need to care about are in "bigWig.h". Below is a commented example. You can see the files under <span class="sb" style="color: #d14;">`test/`</span> for further examples.</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> #include "bigWig.h"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="sb" style="color: #d14;"> int main(int argc, char *argv[]) {</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bigWigFile_t *fp = NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwOverlappingIntervals_t *intervals = NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;"> double *stats = NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(argc != 2) {</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 1;</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Initialize enough space to hold 128KiB (1<<17) of data at a time</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwInit(1<<17) != 0) {</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "Received an error in bwInit\n");</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 1;</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Open the local/remote file</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fp = bwOpen(argv[1], NULL, "r");</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(!fp) {</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "An error occured while opening %s\n", argv[1]);</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 1;</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Get values in a range (0-based, half open) without NAs</span></span>
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<td class="diff-line-num old old_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 0);</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwDestroyOverlappingIntervals(intervals); //Free allocated memory</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Get values in a range (0-based, half open) with NAs</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="sb" style="color: #d14;"> intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 1);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="40" 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">
40
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<td class="diff-line-num new_line old" data-linenumber="9" 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">
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwDestroyOverlappingIntervals(intervals); //Free allocated memory</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="42" 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">
42
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<td class="diff-line-num new_line old" data-linenumber="9" 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">
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Get the full intervals that overlap</span></span>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<td class="diff-line-num new_line old" data-linenumber="9" 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">
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="sb" style="color: #d14;"> intervals = bwGetOverlappingIntervals(fp, "chr1", 10000000, 10000100);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="44" 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">
44
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<td class="diff-line-num new_line old" data-linenumber="9" 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">
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwDestroyOverlappingIntervals(intervals);</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"></span>
</pre>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Get an example statistic - standard deviation</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //We want ~4 bins in the range</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;"> stats = bwStats(fp, "chr1", 10000000, 10000100, 4, dev);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(stats) {</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;"> printf("chr1:10000000-10000100 std. dev.: %f %f %f %f\n", stats[0], stats[1], stats[2], stats[3]);</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;"> free(stats);</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwClose(fp);</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwCleanup();</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 0;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">The only functions and structures that end users need to care about are in "bigWig.h". Below is a commented example. You can see the files under <span class="p">[</span><span class="nv" style="color: #008080;">`test/`</span><span class="p">](</span><span class="sx" style="color: #d14;">./test/</span><span class="p">)</span> for further examples.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">```</span><span class="nl">c</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bigWig.h"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"> <span class="n" style="color: #333;">bigWigFile_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"> <span class="n" style="color: #333;">bwOverlappingIntervals_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Usage: %s {file.bw|URL://path/file.bw}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Initialize enough space to hold 128KiB (1<<17) of data at a time</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwInit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">17</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Received an error in bwInit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"> <span class="p">}</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Open the local/remote file</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwOpen</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"An error occured while opening %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Get values in a range (0-based, half open) without NAs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="markdown"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwGetValues</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000100</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="markdown"> <span class="n" style="color: #333;">bwDestroyOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">intervals</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//Free allocated memory</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Get values in a range (0-based, half open) with NAs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwGetValues</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000100</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"> <span class="n" style="color: #333;">bwDestroyOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">intervals</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//Free allocated memory</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Get the full intervals that overlap</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwGetOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000100</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"> <span class="n" style="color: #333;">bwDestroyOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">intervals</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Get an example statistic - standard deviation</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//We want ~4 bins in the range</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwStats</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000100</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">dev</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"chr1:10000000-10000100 std. dev.: %f %f %f %f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"> <span class="n" style="color: #333;">bwClose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"> <span class="n" style="color: #333;">bwCleanup</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Writing example</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown">N.B., creation of bigBed files is not supported (there are no plans to change this).</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown">Below is an example of how to write bigWig files. You can also find this file under <span class="sb" style="color: #d14;">`test/exampleWrite.c`</span>. Unlike with Kent's tools, you can create bigWig files entry by entry without needing an intermediate wiggle or bedGraph file. Entries in bigWig files are stored in blocks with each entry in a block referring to the same chromosome and having the same type, of which there are three (see the <span class="p">[</span><span class="nv" style="color: #008080;">wiggle specification</span><span class="p">](</span><span class="sx" style="color: #d14;">http://genome.ucsc.edu/goldenpath/help/wiggle.html</span><span class="p">)</span> for more information on this).</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;"> #include "bigWig.h"</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"><span class="sb" style="color: #d14;"> int main(int argc, char *argv[]) {</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bigWigFile_t *fp = NULL;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="sb" style="color: #d14;"> char *chroms[] = {"1", "2"};</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;"> char *chromsUse[] = {"1", "1", "1"};</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="sb" style="color: #d14;"> uint32_t chrLens[] = {1000000, 1500000};</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"><span class="sb" style="color: #d14;"> uint32_t starts[] = {0, 100, 125,</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 200, 220, 230,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 500, 600, 625,</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 700, 800, 850};</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown"><span class="sb" style="color: #d14;"> uint32_t ends[] = {5, 120, 126,</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 205, 226, 231};</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;"> float values[] = {0.0f, 1.0f, 200.0f,</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -2.0f, 150.0f, 25.0f,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 0.0f, 1.0f, 200.0f,</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -2.0f, 150.0f, 25.0f,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -5.0f, -20.0f, 25.0f,</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -5.0f, -20.0f, 25.0f};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </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="markdown"><span class="sb" style="color: #d14;"> if(bwInit(1<<17) != 0) {</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="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "Received an error in bwInit\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 1;</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fp = bwOpen("example_output.bw", NULL, "w");</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(!fp) {</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "An error occurred while opening example_output.bw for writingn\n");</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 1;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Allow up to 10 zoom levels, though fewer will be used in practice</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwCreateHdr(fp, 10)) goto error;</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Create the chromosome lists</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fp->cl = bwCreateChromList(chroms, chrLens, 2);</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(!fp->cl) goto error;</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Write the header</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwWriteHdr(fp)) goto error;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">Below is an example of how to write bigWig files. You can also find this file under <span class="p">[</span><span class="nv" style="color: #008080;">`test/exampleWrite.c`</span><span class="p">](</span><span class="sx" style="color: #d14;">test/exampleWrite.c</span><span class="p">)</span>. Unlike with Kent's tools, you can create bigWig files entry by entry without needing an intermediate wiggle or bedGraph file. Entries in bigWig files are stored in blocks with each entry in a block referring to the same chromosome and having the same type, of which there are three (see the <span class="p">[</span><span class="nv" style="color: #008080;">wiggle specification</span><span class="p">](</span><span class="sx" style="color: #d14;">http://genome.ucsc.edu/goldenpath/help/wiggle.html</span><span class="p">)</span> for more information on this).</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p">```</span><span class="nl">c</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bigWig.h"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"> <span class="n" style="color: #333;">bigWigFile_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chroms</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">};</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chromsUse</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">};</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrLens</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">1000000</span><span class="p">,</span> <span class="mi" style="color: #099;">1500000</span><span class="p">};</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">starts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">125</span><span class="p">,</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"> <span class="mi" style="color: #099;">200</span><span class="p">,</span> <span class="mi" style="color: #099;">220</span><span class="p">,</span> <span class="mi" style="color: #099;">230</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">600</span><span class="p">,</span> <span class="mi" style="color: #099;">625</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"> <span class="mi" style="color: #099;">700</span><span class="p">,</span> <span class="mi" style="color: #099;">800</span><span class="p">,</span> <span class="mi" style="color: #099;">850</span><span class="p">};</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ends</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">120</span><span class="p">,</span> <span class="mi" style="color: #099;">126</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"> <span class="mi" style="color: #099;">205</span><span class="p">,</span> <span class="mi" style="color: #099;">226</span><span class="p">,</span> <span class="mi" style="color: #099;">231</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">values</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">200</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">200</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">20</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">20</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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105
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"> </span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Some example bedGraph-like entries</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;</span></span>
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108
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<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //We can continue appending similarly formatted entries</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="109" 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">
109
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<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //N.B. you can't append a different chromosome (those always go into different</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="110" 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">
110
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<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAppendIntervals(fp, starts+3, ends+3, values+3, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="112" 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">
112
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAddIntervalSpans(fp, "1", starts+6, 20, values+6, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="114" 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">
114
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //We can continue appending similarly formatted entries</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC115" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAppendIntervalSpans(fp, starts+9, values+9, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="116" 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">
116
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Add a new block of fixed-step entries</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="118" 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">
118
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAddIntervalSpanSteps(fp, "1", 900, 20, 30, values+12, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="119" 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">
119
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //The start is then 760, since that's where the previous step ended</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="120" 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">
120
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAppendIntervalSpanSteps(fp, values+15, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="121" 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">
121
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="122" 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">
122
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Add a new chromosome</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="123" 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">
123
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;"> chromsUse[0] = "2";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="124" 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">
124
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;"> chromsUse[1] = "2";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown"><span class="sb" style="color: #d14;"> chromsUse[2] = "2";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC126" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC127" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="128" 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">
128
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Closing the file causes the zoom levels to be created</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwClose(fp);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="130" 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">
130
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC130" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwCleanup();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="131" 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">
131
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC131" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="132" 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">
132
</td>
<td class="diff-line-num new_line old" data-linenumber="88" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC132" class="line" lang="markdown"><span class="sb" style="color: #d14;"> return 0;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="markdown"><span class="sb" style="color: #d14;"> error:</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;"> fprintf(stderr, "Received an error somewhere!\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwClose(fp);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" 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">
137
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<td class="diff-line-num new_line old" data-linenumber="88" 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">
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwCleanup();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="138" 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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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwInit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">17</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Received an error in bwInit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="138" 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">
138
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<td class="diff-line-num new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="139" 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">
139
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<td class="diff-line-num new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="140" 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">
140
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<td class="diff-line-num new_line" data-linenumber="92" 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">
92
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"example_output.bw"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</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="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"An error occurred while opening example_output.bw for writingn</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Allow up to 10 zoom levels, though fewer will be used in practice</span></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwCreateHdr</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Create the chromosome lists</span></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"> <span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwCreateChromList</span><span class="p">(</span><span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">chrLens</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cl</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Write the header</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwWriteHdr</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Some example bedGraph-like entries</span></span>
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<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAddIntervals</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">chromsUse</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//We can continue appending similarly formatted entries</span></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//N.B. you can't append a different chromosome (those always go into different</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAppendIntervals</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAddIntervalSpans</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//We can continue appending similarly formatted entries</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAppendIntervalSpans</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Add a new block of fixed-step entries</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAddIntervalSpanSteps</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="mi" style="color: #099;">900</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//The start is then 760, since that's where the previous step ended</span></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAppendIntervalSpanSteps</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="141" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Add a new chromosome</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"> <span class="n" style="color: #333;">chromsUse</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2"</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"> <span class="n" style="color: #333;">chromsUse</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"> <span class="n" style="color: #333;">chromsUse</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwAddIntervals</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">chromsUse</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Closing the file causes the zoom levels to be created</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"> <span class="n" style="color: #333;">bwClose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"> <span class="n" style="color: #333;">bwCleanup</span><span class="p">();</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="nl">error:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Received an error somewhere!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"> <span class="n" style="color: #333;">bwClose</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"> <span class="n" style="color: #333;">bwCleanup</span><span class="p">();</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"><span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="p">```</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"></span>
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141
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"><span class="gh" style="color: #999;"># Testing file types</span></span>
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142
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"></span>
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143
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown">As of version 0.3.0, this library supports accessing bigBed files, which are related to bigWig files. Applications that need to support both bigWig and bigBed input can use the <span class="sb" style="color: #d14;">`bwIsBigWig`</span> and <span class="sb" style="color: #d14;">`bbIsBigBed`</span> functions to determine if their inputs are bigWig/bigBed files:</span>
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144
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ...code...</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown"><span class="sb" style="color: #d14;"> if(bwIsBigWig(input_file_name, NULL)) {</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //do something</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="sb" style="color: #d14;"> } else if(bbIsBigBed(input_file_name, NULL)) {</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //do something else</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown"><span class="sb" style="color: #d14;"> } else {</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //handle unknown input</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"><span class="p">```</span><span class="nl">c</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="p">...</span><span class="n" style="color: #333;">code</span><span class="p">...</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwIsBigWig</span><span class="p">(</span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//do something</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bbIsBigBed</span><span class="p">(</span><span class="n" style="color: #333;">input_file_name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//do something else</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"><span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//handle unknown input</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="p">```</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="markdown">Note that these two functions rely on the "magic number" at the beginning of each file, which differs between bigWig and bigBed files.</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown"></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">@@ -220,12 +226,14 @@ Regardless of whether a bigWig or bigBed file is being used, the `bwIteratorNext</td>
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown"></span>
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221
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown">A full example is provided in <span class="sb" style="color: #d14;">`tests/testIterator.c`</span>, but a small example of iterating over all bigWig intervals in <span class="sb" style="color: #d14;">`chr1:0-10000000`</span> in chunks of 5 blocks follows:</span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="markdown"><span class="sb" style="color: #d14;"> iter = bwOverlappingIntervalsIterator(fp, "chr1", 0, 10000000, 5);</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="markdown"><span class="sb" style="color: #d14;"> while(iter->data) {</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="markdown"><span class="sb" style="color: #d14;"> //Do stuff with iter->intervals</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="markdown"><span class="sb" style="color: #d14;"> iter = bwIteratorNext(iter);</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="markdown"><span class="sb" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="markdown"><span class="sb" style="color: #d14;"> bwIteratorDestroy(iter);</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="p">```</span><span class="nl">c</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwOverlappingIntervalsIterator</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"><span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//Do stuff with iter->intervals</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bwIteratorNext</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="n" style="color: #333;">bwIteratorDestroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"><span class="gh" style="color: #999;"># A note on bigWig statistics</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="markdown"></span>
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<li id="9aab895775dcc7220eb583d52463759054d493e3">
<a href="https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807#9aab895775dcc7220eb583d52463759054d493e3"><strong>bigWig.h</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">@@ -53,7 +53,7 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*!</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The library version number</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LIBBIGWIG_VERSION 0.4.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LIBBIGWIG_VERSION 0.4.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*!</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * If 1, then this library was compiled with remote file support.</span></span>
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<a href="https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807#b4b53d426209550bb804b2936264ec0aa7750996"><strong>bwRead.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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">@@ -73,7 +73,7 @@ static bwZoomHdr_t *bwReadZoomHdrs(bigWigFile_t *bw) {</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">indexOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bw</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nLevels</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">data</span>Offset</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;"><span class="idiff left right">index</span>Offset</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">zhdr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dataOffset</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807#2da8b51e3330d487a1640608d75f54107f75cf32"><strong>bwValues.c</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">@@ -33,7 +33,7 @@ static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) {</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">malloc</span></span><span class="p"><span class="idiff right">(</span></span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">bwRTree_t</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">calloc</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">bwRTree_t</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">node</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bwRead</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">blockSize</span><span class="p">),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807#0121f0e8888f2302c167fa994f3bfdff833daa69"><strong>io.c</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">@@ -133,7 +133,7 @@ CURLcode urlSeek(URL_t *URL, size_t pos) {</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NOCURL</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//If the location is covered by the buffer then don't seek!</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filePos</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filePos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buf<span class="idiff left right">Size</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filePos</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filePos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buf<span class="idiff left right">Len</span></span><span class="p">)</span> <span class="p">{</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bufLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Otherwise, filePos will get incremented on the next read!</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">URL</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bufPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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