8e09df1bb2
- Update to version 1.12 OBS-URL: https://build.opensuse.org/request/show/893090 OBS-URL: https://build.opensuse.org/package/show/science/bcftools?expand=0&rev=12
78 lines
3.7 KiB
Diff
78 lines
3.7 KiB
Diff
From: toddrme2178@gmail.com
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Date: 2020-02-12
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Subject: Use python3 instead of python2
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The package currently uses the "python" executable, but it should be
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python3 compatible according to the documentation. This patch changes
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all the executables to use "python3" instead of "python".
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diff -Nur bcftools-1.12/doc/bcftools.1 new/doc/bcftools.1
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--- bcftools-1.12/doc/bcftools.1 2021-03-17 10:16:18.000000000 +0100
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+++ new/doc/bcftools.1 2021-05-14 12:40:00.545719382 +0200
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@@ -5773,7 +5773,7 @@
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.nf
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# The final looks can be customized by editing the generated
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# \*(Aqoutdir/plot\&.py\*(Aq script and re\-running manually
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-cd outdir && python plot\&.py && pdflatex summary\&.tex
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+cd outdir && python3 plot\&.py && pdflatex summary\&.tex
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.fi
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.if n \{\
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.RE
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diff -Nur bcftools-1.12/doc/bcftools.html new/doc/bcftools.html
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--- bcftools-1.12/doc/bcftools.html 2021-03-17 10:16:18.000000000 +0100
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+++ new/doc/bcftools.html 2021-05-14 12:40:00.553719441 +0200
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@@ -3171,7 +3171,7 @@
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bcftools stats -s - > file.vchk</pre><pre class="literallayout"># Plot the stats
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plot-vcfstats -p outdir file.vchk</pre><pre class="literallayout"># The final looks can be customized by editing the generated
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# 'outdir/plot.py' script and re-running manually
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-cd outdir && python plot.py && pdflatex summary.tex</pre></div></div><div class="refsect1"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records
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+cd outdir && python3 plot.py && pdflatex summary.tex</pre></div></div><div class="refsect1"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records
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are internally converted into BCF representation. Simple operations, like removing
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a single column from a VCF file, can be therefore done much faster with standard
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UNIX commands, such as <span class="strong"><strong>awk</strong></span> or <span class="strong"><strong>cut</strong></span>.
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diff -Nur bcftools-1.12/doc/bcftools.txt new/doc/bcftools.txt
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--- bcftools-1.12/doc/bcftools.txt 2021-03-10 17:48:14.000000000 +0100
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+++ new/doc/bcftools.txt 2021-05-14 12:40:00.557719471 +0200
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@@ -3278,7 +3278,7 @@
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# The final looks can be customized by editing the generated
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# 'outdir/plot.py' script and re-running manually
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- cd outdir && python plot.py && pdflatex summary.tex
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+ cd outdir && python3 plot.py && pdflatex summary.tex
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--
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PERFORMANCE
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diff -Nur bcftools-1.12/misc/guess-ploidy.py new/misc/guess-ploidy.py
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--- bcftools-1.12/misc/guess-ploidy.py 2019-11-05 15:56:36.000000000 +0100
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+++ new/misc/guess-ploidy.py 2021-05-14 12:40:24.421895595 +0200
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env python
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+#!/usr/bin/python3
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#
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# Plot the output of "bcftools +guess-ploidy -v"
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#
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diff -Nur bcftools-1.12/polysomy.c new/polysomy.c
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--- bcftools-1.12/polysomy.c 2019-05-30 23:56:51.000000000 +0200
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+++ new/polysomy.c 2021-05-14 12:40:24.421895595 +0200
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@@ -253,7 +253,7 @@
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FILE *fp = open_file(&fname,"w","%s/dist.py", args->output_dir);
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//-------- matplotlib script --------------
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fprintf(fp,
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- "#!/usr/bin/env python\n"
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+ "#!/usr/bin/python3\n"
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"#\n"
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"import matplotlib as mpl\n"
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"mpl.use('Agg')\n"
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diff -Nur bcftools-1.12/vcfcnv.c new/vcfcnv.c
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--- bcftools-1.12/vcfcnv.c 2020-02-17 14:05:23.000000000 +0100
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+++ new/vcfcnv.c 2021-05-14 12:40:00.537719323 +0200
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@@ -321,7 +321,7 @@
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{
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if ( th>100 ) return; // create no plots
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- char *cmd = msprintf("python %s -p %f", script, th);
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+ char *cmd = msprintf("python3 %s -p %f", script, th);
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int ret = system(cmd);
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if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
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free(cmd);
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