David Roazen 133085469f Experimental, downsampler-friendly read shard balancer ... -Only used when experimental downsampling is enabled -Persists read iterators across shards, creating a new set only when we've exhausted the current BAM file region(s). This prevents the engine from revisiting regions discarded by the downsamplers / filters, as could happen in the old implementation. -SAMDataSource no longer tracks low-level file positions in experimental mode. Can strip out all related code when the engine fork is collapsed. -Defensive implementation that assumes BAM file regions coming out of the BAM Schedule can overlap; should be able to improve performance if we can prove they cannot possibly overlap. -Tests a bit on the extreme side (~8 minute runtime) for now; will scale these back once confidence in the code is gained		2012-09-21 22:17:58 -04:00
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picard/reference	Fixing bug in fasta .fai generation: trim the contig names to the first whitespace if one appears. We now generate indexes identical to samtools.	2012-08-29 22:36:27 -04:00
samtools	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00