Keep unmapped reads in a separate file. Improvements to relaunch dups…

… script

svn r110

launch.sh

@@ -193,7 +193,7 @@ if [ -z "$earlyexit" ]
 		echo -e "echo Splits done, launching other jobs." >> tmp
 		echo -e "bkill -J ${groupname}_clean2" >> tmp
 		echo "bsub -o $topDir/lsf.out -q $queue -g ${groupname}_clean -w \"done(${groupname}_kill)\" \"echo /broad/aidenlab/neva/neva_scripts/relaunch_dups.sh $flags > $topDir/relaunchme.sh\" " >> tmp
-		echo "bsub -o $topDir/lsf.out -q $queue -g $groupname -w \"done(${groupname}_split)\" -J ${groupname}stats \"source /broad/software/scripts/useuse; reuse Java-1.6; awk -v thresh=1 -f /broad/aidenlab/neva/neva_scripts/mapq.awk $outputdir/merged_nodups.txt > $outputdir/merged_0.txt;   /broad/aidenlab/neva/neva_scripts/statistics.pl -s $site_file -d $outputdir -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; export LC_ALL=en_US.UTF-8; cat $splitdir/*.res.txt | awk -f /broad/aidenlab/neva/neva_scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp /broad/aidenlab/neva/neva_scripts/ LibraryComplexity $outputdir >> $outputdir/inter.txt; /broad/aidenlab/neva/neva_scripts/statistics.pl -s $site_file -d $outputdir -l $ligation -o $outputdir/inter.txt $outputdir/merged_0.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; awk -f /broad/aidenlab/neva/neva_scripts/abnormal.awk $outputdir/abnormal.sam > $outputdir/abnormal.txt\" " >> tmp
+		echo "bsub -o $topDir/lsf.out -q $queue -g $groupname -w \"done(${groupname}_split)\" -J ${groupname}stats \"source /broad/software/scripts/useuse; reuse Java-1.6; awk -v thresh=1 -f /broad/aidenlab/neva/neva_scripts/mapq.awk $outputdir/merged_nodups.txt > $outputdir/merged_0.txt;   /broad/aidenlab/neva/neva_scripts/statistics.pl -s $site_file -d $outputdir -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; export LC_ALL=en_US.UTF-8; cat $splitdir/*.res.txt | awk -f /broad/aidenlab/neva/neva_scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp /broad/aidenlab/neva/neva_scripts/ LibraryComplexity $outputdir >> $outputdir/inter.txt; /broad/aidenlab/neva/neva_scripts/statistics.pl -s $site_file -d $outputdir -l $ligation -o $outputdir/inter.txt $outputdir/merged_0.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f /broad/aidenlab/neva/neva_scripts/abnormal.awk $outputdir/abnormal.sam > $outputdir/abnormal.txt\" " >> tmp
 		echo -e "bsub -o $topDir/lsf.out  -q $queue -R \"rusage[mem=4]\" -g $groupname -w  \"done(${groupname}stats)\" -J ${groupname}hic \" source /broad/software/scripts/useuse; reuse Java-1.6; cut -d' ' -f1,2,3,4,5,6,7,8 $outputdir/merged_0.txt > $outputdir/merged_nodups_small.txt; /broad/aidenlab/HiCTools/hictools pairsToBin $outputdir/merged_nodups_small.txt $outputdir/merged_nodups.bin $genomeID ; /broad/aidenlab/HiCTools/hictools pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m $outputdir/merged_nodups.bin $outputdir/inter.hic $genomeID ; /broad/aidenlab/HiCTools/hictools addNorm $outputdir/inter.hic;  rm $outputdir/merged_0.txt; rm $outputdir/merged_nodups_small.txt; rm $outputdir/merged_nodups.bin ; if [[ $topDir == *MiSeq* ]]; then mkdir $newdir; ln -s $outputdir/inter*.hic $newdir/. ; echo leaf0${newleaf} = ${key}, ${hicdir}, http://iwww.broadinstitute.org/igvdata/hic/files/${hicdir}/inter.hic, 50 >> /broad/aidenlab/hic_files/hicInternalMenu.properties;  fi  \" " >> tmp
 		echo -e "bsub -o $topDir/lsf.out  -q $queue -R \"rusage[mem=4]\" -g $groupname -w  \"done(${groupname}_split)\" -J ${groupname}hic30 \"source /broad/software/scripts/useuse; reuse Java-1.6; awk -v thresh=30 -f /broad/aidenlab/neva/neva_scripts/mapq.awk $outputdir/merged_nodups.txt > $outputdir/merged_30.txt; /broad/aidenlab/neva/neva_scripts/statistics.pl -s $site_file -d $outputdir -l $ligation -o $outputdir/inter_30.txt $outputdir/merged_30.txt; cut -d' ' -f1,2,3,4,5,6,7,8 $outputdir/merged_30.txt > $outputdir/merged_nodups_small_30.txt; /broad/aidenlab/HiCTools/hictools pairsToBin $outputdir/merged_nodups_small_30.txt $outputdir/merged_nodups_30.bin $genomeID; /broad/aidenlab/HiCTools/hictools pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m $outputdir/merged_nodups_30.bin $outputdir/inter_30.hic $genomeID; /broad/aidenlab/HiCTools/hictools addNorm $outputdir/inter_30.hic; rm $outputdir/merged_nodups_small_30.txt; rm $outputdir/merged_nodups_30.bin; rm $outputdir/merged_30.txt; \"" >> tmp
 		bsub < tmp