bcftools/use_python3.patch

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 -Nur bcftools-1.15.1/doc/bcftools.1 new/doc/bcftools.1
--- bcftools-1.15.1/doc/bcftools.1	2022-04-07 17:32:58.000000000 +0200
+++ new/doc/bcftools.1	2022-04-21 17:54:28.011999739 +0200
@@ -5841,7 +5841,7 @@
 .fam C
 # 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
 .fam
 .fi
 .if n .RE
diff -Nur bcftools-1.15.1/doc/bcftools.html new/doc/bcftools.html
--- bcftools-1.15.1/doc/bcftools.html	2022-04-07 17:32:58.000000000 +0200
+++ new/doc/bcftools.html	2022-04-21 17:54:28.011999739 +0200
@@ -4942,7 +4942,7 @@
 <div class="content">
 <pre># 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>
+cd outdir &amp;&amp; python3 plot.py &amp;&amp; pdflatex summary.tex</pre>
 </div>
 </div>
 </div>
diff -Nur bcftools-1.15.1/doc/bcftools.txt new/doc/bcftools.txt
--- bcftools-1.15.1/doc/bcftools.txt	2022-03-03 16:10:50.000000000 +0100
+++ new/doc/bcftools.txt	2022-04-21 17:54:28.011999739 +0200
@@ -3635,7 +3635,7 @@
 
     # 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
 --
 
 
diff -Nur bcftools-1.15.1/misc/guess-ploidy.py new/misc/guess-ploidy.py
--- bcftools-1.15.1/misc/guess-ploidy.py	2021-06-23 12:49:05.000000000 +0200
+++ new/misc/guess-ploidy.py	2022-04-21 17:53:16.863999747 +0200
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 #
 # Plot the output of "bcftools +guess-ploidy -v"
 #
diff -Nur bcftools-1.15.1/vcfcnv.c new/vcfcnv.c
--- bcftools-1.15.1/vcfcnv.c	2022-02-17 13:45:09.000000000 +0100
+++ new/vcfcnv.c	2022-04-21 17:53:54.239999743 +0200
@@ -321,7 +321,7 @@
 {
     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);