hanna 768f865035 Bulletproofing code. If errors are encountering during the run, turn them ... into JDK exceptions whenever possible instead of random core dumps. Don't allow negative values for most of the 'bwa aln' input parameters. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2049 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-14 22:57:16 +00:00
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Makefile	Repackage the aligner for better partitioning. The C aligner, for example, is now	2009-11-13 22:55:27 +00:00
build_linux.sh	More preparation for bwa patch: create a crude, minimal build system to build	2009-11-06 18:41:01 +00:00
build_mac.sh	BWA/C changes have arrived in svn repository. Remove temporary storage from Sting repository.	2009-11-11 16:48:21 +00:00
bwa_gateway.cpp	Fix max edit distance to ensure interface similarity between our aligner and	2009-11-13 22:18:56 +00:00
bwa_gateway.h	Fix max edit distance to ensure interface similarity between our aligner and	2009-11-13 22:18:56 +00:00
org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp	Bulletproofing code. If errors are encountering during the run, turn them	2009-11-14 22:57:16 +00:00
org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h	Repackage the aligner for better partitioning. The C aligner, for example, is now	2009-11-13 22:55:27 +00:00