# HG changeset patch
# User sanbi-uwc
# Date 1525776254 14400
# Node ID f6caa75cb8e03935575f17b660428be6be72d7d8
# Parent  55b17de30a360b1e11026b9531f069f04670a27d
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/freebayes commit 3f4a67a48ec54e9e61e4c44b8d5af3f79b0b3e12

diff -r 55b17de30a36 -r f6caa75cb8e0 freebayes.xml
--- a/freebayes.xml	Sun Apr 22 17:33:17 2018 -0400
+++ b/freebayes.xml	Tue May 08 06:44:14 2018 -0400
@@ -44,7 +44,7 @@
     #else
         ##divide up the regions in the bam file for efficient processing
         #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
-            samtools view -H b_${bam_count}.bam |
+            samtools sort - | samtools view -H b_${bam_count}.bam |
             grep '^@SQ' |
             cut -f 2- |
             awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&