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diff [APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh @ 3:1c699789d6d3 draft

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author alermine
date Wed, 14 Nov 2012 06:02:48 -0500
parents 5d392b477172
children
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--- a/[APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh	Wed Nov 14 06:01:02 2012 -0500
+++ b/[APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh	Wed Nov 14 06:02:48 2012 -0500
@@ -107,7 +107,7 @@
     fi
 
     if [[ $ALIGNER == "sam" && $IFBAM == 0 ]]; then
-       samtools view -S -h $INPUT -b |  $SAMTOOLS_BIN_DIR/samtools sort -m 4000000000 -o - $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
+       samtools view -S -h $INPUT -b | samtools sort -m 4000000000 -o - $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
     fi
 
     if [[ $ALIGNER == "sam" && $IFBAM == 1 ]]; then