Mercurial > repos > devteam > picard1106

annotate fastq2sam_wrapper.sh @ 153:5d881472c379 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
mm
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 21 Jul 2014 16:36:03 -0400
parents 7d0d25eabacb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
101
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
1 #!/bin/bash
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
2
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
3 if [ "$1" == "sam" ]
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
4 then
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
5 output=$2.sam
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
6 else
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
7 output=$2
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
8 fi
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
9
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
10 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5} 2>&1
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
11
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
12 if [ "$1" == "sam" ]
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
13 then
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
14 mv $2.sam $2
7d0d25eabacb Uploaded
devteam
parents:
diff changeset
15 fi