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comparison [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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2:5d392b477172 3:1c699789d6d3
105 if [ -r $INPUT.tmp.tmp.txt ]; then 105 if [ -r $INPUT.tmp.tmp.txt ]; then
106 rm $INPUT.tmp.tmp.txt 106 rm $INPUT.tmp.tmp.txt
107 fi 107 fi
108 108
109 if [[ $ALIGNER == "sam" && $IFBAM == 0 ]]; then 109 if [[ $ALIGNER == "sam" && $IFBAM == 0 ]]; then
110 samtools view -S -h $INPUT -b | $SAMTOOLS_BIN_DIR/samtools sort -m 4000000000 -o - $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG 110 samtools view -S -h $INPUT -b | samtools sort -m 4000000000 -o - $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
111 fi 111 fi
112 112
113 if [[ $ALIGNER == "sam" && $IFBAM == 1 ]]; then 113 if [[ $ALIGNER == "sam" && $IFBAM == 1 ]]; then
114 samtools sort -m 14000000000 -o $INPUT $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG 114 samtools sort -m 14000000000 -o $INPUT $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
115 FILE=$INPUT.tmp.sam 115 FILE=$INPUT.tmp.sam