Mauricio Carneiro d00b2c6599 Adding a synthetic read for filtered data ... * Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data. * Synthetic reads can now have deletions (but not insertions) * New reduced read tag for filtered data synthetic reads *(RF)* * Sliding window header now keeps information of consensus and filtered data * Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads		2011-11-09 20:16:22 -05:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Adding a synthetic read for filtered data	2011-11-09 20:16:22 -05:00