Mercurial > repos > devteam > picard1106

annotate fastq2sam_wrapper.sh @ 143:b2ca2d181fb4 draft

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fixed downsample sam in picard1106 (accept bam)
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 16 Jun 2014 17:38:15 -0400
parents 7d0d25eabacb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2
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3 if [ "$1" == "sam" ]
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4 then
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5 output=$2.sam
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6 else
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7 output=$2
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8 fi
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9
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10 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5} 2>&1
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11
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12 if [ "$1" == "sam" ]
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13 then
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14 mv $2.sam $2
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15 fi