aeff0eed7a
Use native SSE2 intrinsics on i386 as well as x86-64
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Make the native SSE2 code conditional on __SSE2__, which is defined
by GCC/Clang/etc on x86-64 by default and on i386 with -msse2 etc.
2022-06-27 14:15:59 +01:00
50f99b6890
On other platforms, emulate SSE2 SIMD calls using scalar code
2022-06-26 19:38:20 +01:00
b64ccddda7
On ARM, rewrite SSE2 SIMD calls using Neon intrinsics
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Many Intel intrinsics have a corresponding Neon equivalent.
Other cases are more interesting:
* Neon's vmaxvq directly selects the maximum entry in a vector,
so can be used to implement both the __max_16/__max_8 macros
and the _mm_movemask_epi8 early loop exit. Introduce additional
helper macros alongside __max_16/__max_8 so that the early loop
exit can similarly be implemented differently on the two platforms.
* Full-width shifts can be done via vextq. This is defined close to
the ksw_u8()/ksw_i16() functions (rather than in neon_sse.h) as it
implicitly uses one of their local variables.
* ksw_i16() uses saturating *signed* 16-bit operations apart from
_mm_subs_epu16; presumably the data is effectively still signed but
we wish to keep it non-negative. The ARM intrinsics are more careful
about type checking, so this requires an extra U16() helper macro.
2022-06-20 20:43:17 +01:00
b5f4bdae91
Make _mm_load_si128() explicit
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The previous code implicitly caused a load; change it so the load
intrinsic is explicitly invoked, as the others are. (This in fact
makes no difference to the generated code.)
2022-06-17 18:42:07 +01:00
0028f086d8
Merge pull request #355 from clintval/cv_document_new_XB
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Document that the XB tag now contains the mapping quality too
2022-06-03 15:01:14 -04:00
c7c2e6ddf7
Document that the XB tag now contains the mapping quality too
2022-05-19 13:43:22 -04:00
8fdc96b5cf
Merge pull request #263 from jmarshall/std-vars
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Makefile: Use $CPPFLAGS and $LDFLAGS if they are set
2022-03-07 09:50:23 -05:00
be36d981cd
Use $CPPFLAGS and $LDFLAGS if they are set
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The bwa makefile doesn't set these two itself, but the environment
or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS.
Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can
be used to customise the build. Remove $(DFLAGS) from link commands as
these preprocessor options are irrelevant for linking.
2022-03-07 10:59:42 +00:00
59cac0131a
Merge branch 'fulcrumgenomics-feature/add-xa-drop-ratio-option'
2022-03-06 18:22:02 -05:00
49c397d16e
Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option
2022-03-06 18:21:49 -05:00
5d250d35de
Merge pull request #293 from nh13/patch-2
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Output mapping quality with XB
2022-03-06 18:18:45 -05:00
e679702118
Merge pull request #292 from nh13/patch-1
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Document "-u"
2022-03-06 18:16:09 -05:00
4d8fb2ca91
Merge pull request #297 from nh13/patch-3
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Clarify bwa mem -5 option
2022-03-06 18:12:09 -05:00
d26eb2d288
Merge pull request #330 from nh13/patch-4
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Add the mate mapping quality tag
2022-03-06 18:07:01 -05:00
4a18837bd2
Merge pull request #336 from nh13/patch-5
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Add the header line to the output SAM
2022-03-06 18:06:38 -05:00
d47f12cddc
Merge pull request #343 from nh13/patch-7
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Update bwa.1 to remove ancient reference to picard
2022-03-06 18:05:46 -05:00
e43eace9e5
Update bwa.1
2022-02-18 13:36:09 -08:00
56026158d8
Add the header line to the output SAM
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In particular, this defines the output SAM to be unsorted BUT also query grouped. The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.
2021-12-14 08:02:05 -07:00
f5e83701ab
Add the mate mapping quality tag
2021-07-21 11:12:27 -07:00
d587a9561b
fixed wrong Markdown format in README
2021-05-10 12:48:45 -04:00
b1ab735f7c
updated to Github CI status
2021-05-10 12:47:13 -04:00
7fe5a14058
Merge pull request #325 from jmarshall/ci
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Use GitHub Actions instead of Travis CI
2021-05-10 12:44:43 -04:00
d27d6a520b
Convert Travis CI to GitHub Actions
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Make an equivalent GitHub Actions workflow that tests compilation
with both GCC and Clang.
2021-05-09 22:54:58 +01:00
87e42dbe32
added code of conduct
2021-04-22 17:35:37 -04:00
ddbd5f7fb7
Removed the debug output; resolves #320
2021-03-09 08:56:52 -05:00
5b96937edc
deprecate bwasw
2021-03-09 00:52:20 -05:00
e2dbfe60e3
output more memory information
2021-02-23 10:43:41 -05:00
d422bdbed9
debug flag to measure memory
2021-02-22 23:26:03 -05:00
b58da139c3
Clarify bwa mem -5 option
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Clarify that the -5 bwa mem option chooses the alignment that starts earliest in the read relative to the read/sequencing order, not genomic coordinate order
2020-08-18 23:01:43 -07:00
34caf50d46
allow the user to specify the XA drop ratio via the -z option
2020-08-12 09:01:44 -07:00
9cbbd6bf94
Update fastmap.c
2020-08-12 08:51:19 -07:00
f717ea1318
Output mapping quality with XB
2020-08-06 10:10:58 -07:00
1a11a6f4b9
Document "-u"
2020-08-06 10:08:29 -07:00
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
John Marshall
Heng Li
clintval
John Marshall
Heng Li
Nils Homer
Nils Homer
Heng Li
David Seifert
Imran Haque