asivache b4136b6d6e a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-13 04:49:19 +00:00
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src/org/broadinstitute/sting	a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg	2009-04-13 04:49:19 +00:00
test/org/broadinstitute/sting	Added basic performance testing so I can make sure concurrent access doesn't slow down overall fasta access.	2009-04-12 18:05:56 +00:00