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resync
prefiltering seems to work
wip - prefiltering fix
working, writing rejected.bam
almost working with bam all over
prep_reads now writes bam
wip -- still errors in logs!
wip: prep_reads from/to BAM
wip
updated
massive update with Daehwan's work
wip - SplicedSAMHitFactory() still not implemented
first attempt at accepting different Color qvlen in prep_reads
adding tophat source work
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