d422bdbed9
debug flag to measure memory
2021-02-22 23:26:03 -05:00
94ff6b297a
added the MIT license header to main.c
2020-07-02 13:49:42 -04:00
d13c2af9bd
Merge branch 'master' of github.com:lh3/bwa
2020-07-01 23:02:31 -04:00
02a9add042
added MIT license to some non-GPL source files
2020-07-01 23:02:01 -04:00
3112df7100
Merge pull request #267 from SoapGentoo/fixes
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GCC 10 and Makefile fixes
2020-03-23 08:56:40 -04:00
2f82fe897a
Fix building against GCC 10
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* GCC 10 defaults to `-fno-common`, which makes C behave
more like C++ in that you can only ever have one definition
of an object per executable.
2020-02-26 13:24:17 +01:00
e8e2803a3d
updated badges
2019-07-09 15:44:34 -04:00
9b12309015
mention bwa-mem2
2019-07-09 10:25:57 -04:00
cd29a7cb54
r1198: exit if .alt is malformatted
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Resolves #232
2019-01-23 13:28:11 -05:00
e4d7a94252
Merge remote-tracking branch 'origin/master'
2018-04-10 15:01:35 -04:00
f9294c0593
Merge pull request #190 from ihaque-freenome/bwa-postalt-fix
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Bug/patch: bwa-postalt.js writes invalid output for SAM input that is an exact multiple of 65536 bytes in length
2018-04-07 18:03:10 -04:00
27dd1da702
Exclude empty SAM lines in bounds check for ALT postprocessor
2018-04-07 07:47:32 +00:00
11d53b06fb
Merge branch 'dev' into XB
2018-04-02 10:47:45 -04:00
eb7dbc1429
optionally write XB to include alignment score
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request from 4DN-DCIC
2018-04-02 10:43:41 -04:00
fde1fd7ce3
emphasize pacbio and nanopore
2017-11-06 19:51:01 -05:00
eef04271e6
wording changes
2017-11-06 19:49:19 -05:00
1a2b0c001a
fixed a typo in link
2017-11-06 19:43:02 -05:00
824e00e7ac
formatting change
2017-11-06 19:41:53 -05:00
ab64326ae6
claim bwa-mem long-read mode deprecated
2017-11-06 19:40:42 -05:00
9f26bfcc77
Released bwa-0.7.17 (r1188)
2017-10-23 13:10:17 -04:00
b582816211
r1187: a typo in command line help
2017-09-26 09:35:19 -04:00
340babdd67
r1185: don't lower supp mapq with -5
2017-09-11 09:58:41 -04:00
a9c688ac92
r1181: fixed a segfault ( #145 ) due to ( #138 )
2017-07-31 07:55:35 -04:00
47d9fb27d7
Release 0.7.16-r1180
2017-07-30 22:35:38 -04:00
5d15c8b09f
Merge pull request #129 from lexentbio/bwakit_fix_sort
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Fix output file parameter for samtools sort
2017-07-30 19:14:09 -04:00
950ea8cf40
Merge pull request #138 from nh13/nh_mem_mate_cigar
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Mem should set the mate cigar tag.
2017-07-30 19:05:47 -04:00
83260ccb10
Merge pull request #60 from jdagilliland/typo
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Typos, doc improvements in man page
2017-07-30 18:59:11 -04:00
1eee77ad93
Merge pull request #84 from jblachly/readgroupfix
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Forbid literal TAB control characters in @RG line
2017-07-30 18:56:39 -04:00
24a8d66481
removed drone.io
2017-07-30 18:49:06 -04:00
89a5c0c5c8
moved BWTFree() into BWTIncFree()
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BWTFree() is not for build. Only BWTIncFree() is needed.
2017-07-30 18:47:03 -04:00
0976272d99
Merge pull request #139 from jmarshall/fixes
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Various collected fixes (updated versions of several existing PRs)
2017-07-30 18:36:07 -04:00
a54e76945e
Merge pull request #70 from rmzelle/patch-1
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Update README.md
2017-07-30 17:01:27 -04:00
31bf49d814
Merge pull request #96 from jpfeil/master
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Add -M option to run-bwamem
2017-07-30 16:57:30 -04:00
498973642f
Merge pull request #123 from bwlang/patch-1
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updates grch38 URL
2017-07-30 16:55:39 -04:00
87ed015b24
Merge pull request #141 from jmarshall/bwasw-nan
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Fail to infer insert size distribution when no pairs are within boundaries (re issue 108)
2017-07-30 16:53:04 -04:00
c56c2e4677
Several trivial Debian patches
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[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling
[Fabian Klötzl]
change printing as size_t is unsigned
2017-07-04 21:24:15 +01:00
3b96dcee7f
Mem should set the mate cigar tag.
2017-07-03 08:51:00 -07:00
bcb475cd03
In bsw2_stat(), fail to infer when no pairs are within boundaries
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Just as we set r.failed and return early if there are no high-quality
read pairs at all, also do so if there are none within the calculated
boundaries. This avoids returning avg=NAN std=NAN, which leads to
malloc(INFINITY) and a crash; fixes #108 .
2017-07-03 13:42:11 +01:00
690649872b
Copy the whole kstring_t even if it contains NULs
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FASTQ files containing NULs are invalid but should not cause bwa to
crash, as it does if the quality line contains a NUL. Fixes #122 .
2017-06-30 12:46:56 +01:00
a61b1dc610
Expand tot_seqs variable to long long
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This counter is only used in a log message. Fixes #131 .
2017-06-29 15:36:46 +01:00
5ede7eb981
Update README.md
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Correct header formatting, fix some typos in headers
2017-06-28 12:07:27 +01:00
bc58bf265d
Add "bwa mem -o FILE" synonym and documentation
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As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.
2017-06-27 17:05:44 +01:00
d28da05f36
Added option to write output to file
2017-06-27 16:47:13 +01:00
ab3a92bc73
Prevent Clang warnings on abs() and fabs() calls
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In the bwa.c and bwase.c calls, rlen is an int64_t returned from
bns_get_seq() and is the number of reference bases covered by the
alignment; l_query/len is an int and the query length of the alignment;
and the result is an int given to an int parameter of ksw_global[2]().
As even the result is int and as rlen is effectively bounded by the
maximum length of a reference sequence, we maintain the status quo in
this code and simply cast rlen to int to silence Clang's "use llabs()"
(llabs() would not be a great answer given an int64_t anyway).
The bwtsw2_pair.c call needs to remain fabs() so both divisions are
done in floating point; cast to double to prevent Clang suggesting
changing the call to integer abs().
2017-06-26 10:45:13 +01:00
05c501332c
Merge branch 'dev'
2017-06-08 16:06:37 -04:00
298284d754
r1144: output debugging message to stderr
2017-06-08 16:06:13 -04:00
7a77cc4785
Fix output file parameter for samtools sort
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samtools sort v0.7.15+ requires -o flag to specify the output file
2017-05-18 15:42:25 -07:00
6a5caf764f
Fixed BWTIncFree() memory leaks
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[Based on PR #37 with the additions below.]
Don't free non-malloced items in BWTFree(). If BWTCreate() is ever
called with a non-NULL decodeTable, BWTFree() will need to not free
decodeTable -- see FIXME comment.
Close packedFile in BWTIncConstructFromPacked() in the normal case.
Ignore it in error cases, as they immediately call exit() anyway.
2017-05-12 16:34:57 +01:00
1972a97813
Only realloc(pac,...) if it needs to be made larger
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Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.
Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file. Fixes #54 .
2017-05-10 19:47:12 +01:00
6442d009cd
updates grch38 URL
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simple URL update for grch38
fixes #111 , #115
grch37 link is still valid
2017-04-27 08:40:48 -04:00
Heng Li
Heng Li
David Seifert
Imran Haque
Andreas Tille
Nils Homer
John Marshall
Rintze M. Zelle
José Manuel Abuín Mosquera
Ram Yalamanchili
Gwen Ives
Brad Langhorst