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
557d50c7e1
r335: fixed a compiling error
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Caused by the last change
2013-03-06 21:57:13 -05:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
6230f86799
merged bwtmisc.c to bwtindex.c
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bwtmisc.c implements routines related to indexing
2013-02-22 17:23:34 -05:00
6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
55f1b36534
New wrapper for gzclose; added err_fflush calls and made it call fsync too.
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Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.
Put in some more err_fflush calls before files being written are closed.
Made err_fflush call fsync. This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned. If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
2013-01-03 16:57:37 +00:00
b081ac9b8b
Use wrapper functions to catch system errors
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Use the wrapper functions in utils.c plus a few extra bits of error
checking code to catch system errors and exit non-zero when they occur.
2012-12-16 10:34:57 +00:00
c875085b2b
do not use .64 suffix by default
2012-03-29 12:31:01 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
dec584d50b
fixed a long-existing bug in trimming
2011-11-23 23:11:50 -05:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
66629512d9
more carefully computed the availableWords
2011-10-20 23:49:03 -04:00
46123639cf
removed reverse pac; bwa is not working right now
2011-10-20 12:09:35 -04:00
72563c38f3
automatically choose the algorithm for BWT
2011-06-09 17:33:25 -04:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Rob Davies
Heng Li
Heng Li