Fixed bug in fastq QUAL output being set to SEQ#2
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fixed typo bug error in the conditions. 2nd condition was setting the QUAL to data from SEQ and thus creating a mangeled fastq output file which caused problems with the next phase alignment output
added output to total connections in final report
replaced all building of #intvlslongall with function longIntervalsToConnections(intvlslong) also added count of nonconreads
original design loads everything in memory and creates unneeded internmediate storage when alignments or read-groups can be processed immeadiately. New design requires QNAME sorted input and uses pysam so input can be .bam files and all output are as .bam files to reduce disk storage. still work in progress
still need to do more testing though
now it can read both sam and bam input files writes out a bam file and has nice arguments interface
- changed all print to logmsg - removed all the old sam-line code and cleaned up
Minor fixes on crssant3.py
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fixed typo bug error in the conditions. 2nd condition was setting the QUAL to data from SEQ and thus creating a mangeled fastq output file which caused problems with the next phase alignment output