Script to run from BAM to SAM to RAM, to test timings and compression.

Author: FonsRademakers

00_run_bamtosamtoram.sh

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+#
+# Script to convert a BAM to a SAM to a RAM file.
+#
+#
+# Best is to cut and paste the desired line from the script.
+#
+# Author: Fons Rademakers, 26/8/17.
+#
+fileid=$1
+
+bamdir=/eos/genome/local/14007a/original_BAM
+samdir=/data3/rdm
+ramdir=../data
+
+bam=$bamdir/$fileid.bam
+sam=$samdir/$fileid.sam
+ram=$ramdir/$fileid.root
+log1=$fileid-1.log
+log2=$fileid-2.log
+
+cd /data/rdm/root
+source  bin/thisroot.sh
+cd ../ramtools
+
+date
+../samtools-1.7/samtools view -h -o $sam $bam
+date
+root.exe -b "samtoram.C+(\"$sam\",\"$ram\")"
+date
+
+#nohup ../samtools-1.7/samtools view -h -o $sam $bam >& $log1 &
+#nohup root.exe -b "samtoram.C+(\"$sam\",\"$ram\")" >& $log2 &
+
+#nohup root.exe -b "samtoram.C+(\"../data/6148s10.sam\",\"../data/6148s10.root\")" >& 6148s10.log &
+
+#nohup root.exe -b "samtoram.C+(\"../data/6148s10.sam\",\"../data/6148s10-lz4.root\",true,true,true,ROOT::kLZ4)" >& 6148s10-lz4.log &