# HG changeset patch
# User fcaramia
# Date 1357710353 18000
# Node ID 22f35f830f488989f36abc7b764c7917750d8c43
# Parent  a72948f2c8c75a574b870838ae3062df9cb4ae3c
Uploaded

diff -r a72948f2c8c7 -r 22f35f830f48 alignCustomAmplicon/alignCustomAmplicon.pl
--- a/alignCustomAmplicon/alignCustomAmplicon.pl	Wed Jan 09 00:36:07 2013 -0500
+++ b/alignCustomAmplicon/alignCustomAmplicon.pl	Wed Jan 09 00:45:53 2013 -0500
@@ -143,6 +143,7 @@
 			-r		do not create stats report
 			-s		sort the bam file
 			-v		verbose progress
+			-j	STR	picard jar
 ) if(@ARGV != 4);
 
 my $Script = 'alignCustomAmplicon';
@@ -172,6 +173,12 @@
 	print "Appending To Log File $now\n\n";
 }
 
+if (defined $OPTIONS{j})
+{
+	my $JAR = $OPTIONS{j};
+
+}
+
 # print version of this script
 print "Using $Script version $version \n\n";
 
@@ -449,7 +456,7 @@
 
 # sort the bam file
 if(defined $OPTIONS{s}) {
-	system("MergeSamFiles.sh  MAX_RECORDS_IN_RAM=2000000 I=$bam_to_sort O=$bamfile_out VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true");
+	system("java -Xmx8g -jar $JAR  MAX_RECORDS_IN_RAM=2000000 I=$bam_to_sort O=$bamfile_out VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true");
 	unlink $bam_to_sort;
 }