0aa7e0a402
Ensure exit status of 1 if given invalid options or index files are not found.
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Added missing default cases in option scanning.
Ensure exit value is 1 if bwa_idx_load or bwa_idx_infer_prefix fail.
These changes extend the previous one, which only fixed the mem aligner.
2013-04-29 13:58:28 +01:00
aabd990e8f
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
503ca9ed2e
r339: pemerge - expose some settings to CLI
2013-03-07 11:22:19 -05:00
1cadfa1552
r338: pemerge - fixed memory leaks; multithreading
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pemerge is actually quite slow.
2013-03-07 11:14:52 -05:00
72817b664e
r336: fine tuning pemerge
2013-03-06 23:38:07 -05:00
042e1f4442
r334: added pemerge to bwa
2013-03-06 21:55:02 -05:00
773b86331b
De-overlap paired-end reads
2013-03-06 19:23:45 -05:00
Rob Davies
Heng Li