Mercurial > repos > devteam > picard1106

annotate mergevcf_wrapper.sh @ 111:83c7b76f0477 draft

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author devteam
date Tue, 25 Feb 2014 01:03:19 -0500
parents c803b1068fa6
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1 #!/bin/bash
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2 #index all vcfs
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3 args=""
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4 for file in ${*:2}
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5 do
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6 cp $file $file.vcf
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7 java -Xmx1500m -jar `dirname $0`/igvtools.jar index $file.vcf
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8 args="$args I=$file.vcf"
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9 done
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10
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11 eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeVcfs.jar QUIET=True O=$1 $args
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12
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13 for file in ${*:2}
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14 do
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15 rm -f $file.vcf
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16 rm -f $file.vcf.idx
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17 done