Create properties.prop

POMP-DETECT/properties.prop

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+(1) INDEX FOLDER PATH 
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/MAIN_INDEX/chr
+(2) MAP FILE PATH
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/MAP/map_50.sam
+(3) UMRQ FILE PATH
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/MAP/umrs_50.fq
+(4) UMRS FILE PATH
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/MAP/umrs_50.fa
+(5) READS FILE PATH
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/READS/50.1.fastq
+(6) COVERAGE FILE PATH
+/home/sus11005/Data/CODE/SPLICED/DATA/NEW/MAP/coverage_50.cov
+(7) NUMBER OF MISMATHES FOR FULL ALIGBMENT
+2
+(8) NUMBER OF MISMATCHES FOR GAPPED ALIGNMENT
+1
+(9) MAX NUMBER OF ALIGNMENT
+100
+(10) NUMBER OF THREADS TO BE USED BY BOWTIE
+10
+(11) LENGTH OF CONSENSUS
+108
+(12) NAME OF THE SEQUENCE
+chr1
+(13) PRE-PROCESS
+off
+(14) HAMMING DISTANCE THRESHOLD
+1.2
+(15) SEARCH SPACE LENGTH
+60000
+(16) MAX RELATIVE ALIGNMENT
+10
+(17) SEQUENCE FILE FOLDER
+/home/sus11005/Data/CODE/ERGC/TAR/HG19/
+(18) OVERLAP LENGTH
+48
+(19) OVERLAP HAMMING DISTANCE
+2
+(20) NUMBER OF THREADS TO BE USED BY POMP
+1
+