File use_python3.patch of Package bcftools

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File use_python3.patch of Package bcftools (Revision c569f720d425da5ff7923444fec315d8)

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From: toddrme2178@gmail.com
Date: 2020-02-12
Subject: Use python3 instead of python2

The package currently uses the "python" executable, but it should be
python3 compatible according to the documentation.  This patch changes
all the executables to use "python3" instead of "python".

diff -U 3 -H -w -E -d -r -N -- a/doc/bcftools.1 b/doc/bcftools.1
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -5440,7 +5440,7 @@
 .nf
 # The final looks can be customized by editing the generated
 # \*(Aqoutdir/plot\&.py\*(Aq script and re\-running manually
-cd outdir && python plot\&.py && pdflatex summary\&.tex
+cd outdir && python3 plot\&.py && pdflatex summary\&.tex
 .fi
 .if n \{\
 .RE

diff -U 3 -H -w -E -d -r -N -- a/doc/bcftools.html b/doc/bcftools.html
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -3012,7 +3012,7 @@
 bcftools stats -s - &gt; file.vchk</pre><pre class="literallayout"># Plot the stats
 plot-vcfstats -p outdir file.vchk</pre><pre class="literallayout"># The final looks can be customized by editing the generated
 # 'outdir/plot.py' script and re-running manually
-cd outdir &amp;&amp; python plot.py &amp;&amp; pdflatex summary.tex</pre></div></div><div class="refsect1" title="PERFORMANCE"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records
+cd outdir &amp;&amp; python3 plot.py &amp;&amp; pdflatex summary.tex</pre></div></div><div class="refsect1" title="PERFORMANCE"><a id="_performance"></a><h2>PERFORMANCE</h2><p>HTSlib was designed with BCF format in mind. When parsing VCF files, all records
 are internally converted into BCF representation. Simple operations, like removing
 a single column from a VCF file, can be therefore done much faster with standard
 UNIX commands, such as <span class="strong"><strong>awk</strong></span> or <span class="strong"><strong>cut</strong></span>.

diff -U 3 -H -w -E -d -r -N -- a/doc/bcftools.txt b/doc/bcftools.txt
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -3101,7 +3101,7 @@
 
     # The final looks can be customized by editing the generated
     # 'outdir/plot.py' script and re-running manually
-    cd outdir && python plot.py && pdflatex summary.tex
+    cd outdir && python3 plot.py && pdflatex summary.tex
 --
 
 PERFORMANCE

diff -U 3 -H -w -E -d -r -N -- a/polysomy.c b/polysomy.c
--- a/polysomy.c
+++ b/polysomy.c
@@ -253,7 +253,7 @@
     FILE *fp = open_file(&fname,"w","%s/dist.py", args->output_dir);
 //-------- matplotlib script --------------
     fprintf(fp,
-        "#!/usr/bin/env python\n"
+        "#!/usr/bin/python3\n"
         "#\n"
         "import matplotlib as mpl\n"
         "mpl.use('Agg')\n"

diff -U 3 -H -w -E -d -r -N -- a/vcfcnv.c b/vcfcnv.c
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -320,7 +320,7 @@
 {
     if ( th>100 ) return;   // create no plots
 
-    char *cmd = msprintf("python %s -p %f", script, th);
+    char *cmd = msprintf("python3 %s -p %f", script, th);
     int ret = system(cmd);
     if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
     free(cmd);

diff -U 3 -H -w -E -d -r -N -- a/vcfgtcheck.c b/vcfgtcheck.c
--- a/vcfgtcheck.c
+++ b/vcfgtcheck.c
@@ -60,7 +60,7 @@
 {
     mkdir_p(script);
     int len = strlen(script);
-    char *cmd = !strcmp(".py",script+len-3) ? msprintf("python %s", script) : msprintf("python %s.py", script);
+    char *cmd = !strcmp(".py",script+len-3) ? msprintf("python3 %s", script) : msprintf("python3 %s.py", script);
     int ret = system(cmd);
     if ( ret ) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
     free(cmd);

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File use_python3.patch of Package bcftools (Revision c569f720d425da5ff7923444fec315d8)

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