forked from samtools/samtools
/
ChangeLog.old
3875 lines (2811 loc) · 114 KB
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ChangeLog.old
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commit db2ad3e19068cbafde72ecde75d0638bbb3598ba
Author: Heng Li <lh3@live.co.uk>
Date: Thu Feb 16 14:45:17 2012 -0500
removed downsample.c
commit 6c55c576903992c6fef148fe3b606fbc8bd10655
Author: Heng Li <lh3@live.co.uk>
Date: Thu Feb 16 14:45:06 2012 -0500
print to output
commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1
Author: Heng Li <lh3@live.co.uk>
Date: Thu Feb 16 14:39:34 2012 -0500
removed sample
Downsampling already exists in "view". View also keeps pairing while "sample" does not.
commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba
Merge: 2daad7b accf026
Author: Heng Li <lh3@live.co.uk>
Date: Thu Feb 16 14:22:15 2012 -0500
Merge branch 'master' of github.com:lh3/samtools
commit accf0260fd1117e10047344345d40b31a9ec31bb
Merge: 9134e0d c554160
Author: Heng Li <lh3@me.com>
Date: Thu Feb 16 11:21:14 2012 -0800
Merge pull request #8 from nh13/master
Patches
commit c554160df16ec7748cfdda4c7b54c641be7b809f
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 14:06:52 2012 -0500
* more README.md work
commit 2a81ffe349208d917666808fbc9f3041e0cb57de
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 14:06:10 2012 -0500
* more README work
commit fb3125f732715f62cded8685a23a002a96ce009b
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 14:05:19 2012 -0500
* more README work
commit 444d41002c37e1c3d0f9208b4a88126c47276386
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 14:02:13 2012 -0500
* updating README
commit dec53cb1043fe7efadfde75fa2fd39b76de22e54
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 13:55:01 2012 -0500
updating the README for markdown syntax
commit 798da18c346dca8ec6005582a0ddb1d5420b04ca
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 13:48:35 2012 -0500
adding a README with the current differences between this repository and
the official one
commit 4d22d86c0f28636662f2144a88cd168e104c4275
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 13:35:03 2012 -0500
adding "samtools sample" to the main
commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 13:33:51 2012 -0500
* removing some compile flags to work with OS X
commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:47:14 2012 -0500
Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit fef53330416631690f60fdff42b6e43d764170dc
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:44:59 2012 -0500
Catch and report invalid BAM header, instead of segfaulting later on.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:44:16 2012 -0500
Add downsample to examples.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:43:48 2012 -0500
Adjust for leading hard clip on colorspace reads.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:42:52 2012 -0500
Add samtools sample command, contributed by Davide Cittaro <davide.cittaro@ifom-ieo-campus.it>.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 2a804f3379748aeba944f1dec306dd726ff3235e
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:42:07 2012 -0500
Add samtools qa command, contributed by Roman Valls Guimera <roman.valls.guimera@scilifelab.se>.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:39:08 2012 -0500
Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 6e7df604025f6a86881bf7f4a16f30e15d31538a
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:31:15 2012 -0500
Allow max_mem for sort to be specified with units.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit f12ebcaf6e60d34180a27d70e09b743cef140b98
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:29:11 2012 -0500
Allow user defined [lowercase] tags in header elements.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 50b931fa3312dc109537a4260698ddecd0f06a05
Author: Jonathan Manning <jonathan.manning@lifetech.com>
Date: Thu Feb 16 10:27:11 2012 -0500
Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get.
Signed-off-by: Nils Homer <nils.homer@lifetech.com>
commit 5e729da5190949a813d20d329eab7ddb661816bd
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 10:31:48 2012 -0500
* fixing overflow/underflow in integer parsing
commit fa50a4330b9abedaf07c26e13d31f05e57f1d319
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 10:30:40 2012 -0500
* updating help message for samtools depth
commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4
Author: Nils Homer <nils.homer@lifetech.com>
Date: Thu Feb 16 10:29:32 2012 -0500
* adding support for outputting a circos histogram file in "samtools depth". Use
the "-c/-B" options.
commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3
Author: Heng Li <lh3@live.co.uk>
Date: Thu Feb 16 09:31:57 2012 -0500
bugfix: wrong SP; missing DV in the VCF hdr
commit 9134e0d5047c281ef3bd53da91771d4814a5131c
Author: Heng Li <lh3@live.co.uk>
Date: Wed Feb 8 11:19:12 2012 -0500
missing support of DV
commit 34ebf12078c1d1015a0b8b9a9221243a60b22893
Author: Heng Li <lh3@live.co.uk>
Date: Wed Feb 8 11:08:56 2012 -0500
new BCF DV format: number of variant reads
commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jan 10 10:30:27 2012 -0500
scale depth to quality (hidden option)
commit 704473e14668333ecaca5fb7b238af405c43e3b1
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jan 10 10:18:17 2012 -0500
really nothing
commit 01b307fd287962372bbf07461c88b54f41636817
Author: Heng Li <lh3@live.co.uk>
Date: Wed Dec 7 13:07:42 2011 -0500
added an example containing 'B'
commit c678791f0451ceb9205c1ab5c52c84641863c99a
Author: Heng Li <lh3@live.co.uk>
Date: Sat Dec 3 12:10:30 2011 -0500
'B' now moves backward w.r.t. the query
commit 152119bc06a073933ca830e8e1407538e44626cc
Author: Heng Li <lh3@live.co.uk>
Date: Fri Dec 2 10:50:12 2011 -0500
better consensus; a little more robust
commit 454da4754ac503edda5b1329b67757d797e46e07
Author: Heng Li <lh3@live.co.uk>
Date: Fri Dec 2 00:20:22 2011 -0500
in pileup call remove_B()
commit ff2bcac1cc078ba1879f18c89cfae314439d7086
Author: Heng Li <lh3@live.co.uk>
Date: Fri Dec 2 00:17:32 2011 -0500
working on a few toy examples
commit 745ca7260158d6df7897b52598033ffb055a9e4f
Author: Heng Li <lh3@live.co.uk>
Date: Thu Dec 1 22:55:39 2011 -0500
bam_remove_B(); not tested
commit 07e4cdc7300abfcc82e03105b4689f95cab551cd
Author: Heng Li <lh3@live.co.uk>
Date: Thu Nov 10 12:58:55 2011 -0500
baseQ threshold on plain pipleup; removed -E
commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2
Author: Heng Li <lh3@live.co.uk>
Date: Wed Oct 19 09:28:04 2011 -0400
fixed two gcc warnings
commit a632457b4c4adc50d833b56b5a5231feafaf8193
Author: Heng Li <lh3@live.co.uk>
Date: Tue Oct 4 10:13:23 2011 -0400
change size_t to uint32_t in bam_header_t
This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon.
commit af31bf5a78aea03baf6eb90fe50076549d499f6e
Author: Heng Li <lh3@live.co.uk>
Date: Mon Sep 26 20:17:57 2011 -0400
rename pad2unpad to depad
commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 23 01:22:40 2011 -0400
convert padded BAM to unpadded BAM
commit adb9e2342b7b7501d9527d3c23afab10469ae2c6
Author: Heng Li <lh3@live.co.uk>
Date: Wed Sep 7 11:40:50 2011 -0400
generate template cigar with "fixmate"
commit 46e5ab445a0fe880216cbc0daf1225725b569d7a
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 2 12:50:18 2011 -0400
update kseq.h to the latest version
commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 2 12:44:45 2011 -0400
Release samtools-0.1.18
commit aa06bdadb2d109a79f927f478102f96a1f5fd258
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 2 12:14:17 2011 -0400
updated the revision number
commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f
Merge: 19ff1d3 aebab30
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 2 12:13:08 2011 -0400
Merge https://github.com/lh3/samtools into reduce
Conflicts:
bam_md.c
Fixed a few typos in the merge
commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a
Merge: c2c63d0 da62663
Author: Heng Li <lh3@live.co.uk>
Date: Fri Sep 2 09:03:49 2011 -0700
Merge pull request #4 from peterjc/x_equals2
Implement basic support for =/X CIGAR operations
commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2
Author: Heng Li <lh3@live.co.uk>
Date: Thu Aug 25 16:38:12 2011 -0400
reduce BAM size (experimental)
commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d
Author: peterjc <p.j.a.cock@googlemail.com>
Date: Mon Aug 22 06:58:08 2011 +0100
Support =/X CIGAR operations (treated like M)
commit 461d8003529db77a4d5ecbd108312e868b051a3d
Author: peterjc <p.j.a.cock@googlemail.com>
Date: Mon Aug 22 05:52:56 2011 +0100
Define CIGAR equals and X operationss (7 and 8)
commit c2c63d067113baab41f3bc35fb28f4f00578accb
Merge: 7ab3ef3 9a0ed9a
Author: Heng Li <lh3@live.co.uk>
Date: Thu Aug 18 17:21:54 2011 -0700
Merge pull request #3 from peterjc/x_equals
Accept SAM files using = in CIGAR (treats X and = as M)
commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5
Author: peterjc <p.j.a.cock@googlemail.com>
Date: Thu Aug 18 19:28:52 2011 +0100
Accept SAM files using = in CIGAR (treats X and = as M)
commit 7ab3ef388c1eb34d7912fd70cc5656c955240263
Author: Heng Li <lh3@live.co.uk>
Date: Mon Aug 8 10:22:22 2011 -0400
bugfix: indexing takes huge memory
This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix.
commit a3f6738593e944354a8f75306687d8b3acf08bf1
Merge: a8bdca9 bc67ea2
Author: Heng Li <lh3@live.co.uk>
Date: Mon Aug 8 09:52:26 2011 -0400
Merge branch 'master' of github.com:lh3/samtools
commit bc67ea225da653f36a70b38382d6111dd494f659
Author: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu Jul 28 20:03:16 2011 +0100
Variant Distance Bias
commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf
Author: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue Jul 26 09:57:37 2011 +0100
If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead.
commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b
Author: Heng Li <lh3@live.co.uk>
Date: Mon Jul 25 10:10:55 2011 -0400
bugfix: LRT2=nan
commit 0afe33137d046a3e849eeb4a54590f27cbad4228
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 22 21:55:38 2011 -0400
fixed a bug/typo
commit 62d5849658c10222d40308c6b53ab4f99a448494
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 15 16:04:19 2011 -0400
allow to set see in subsampling
commit 5f46243824cc9435b167973e1d51e13128794ea1
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 15 15:54:47 2011 -0400
support subsampling
commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 15 15:53:38 2011 -0400
support indels
commit f31c162926d6f43e8b60171789a258d02e1f9be5
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jul 7 17:02:33 2011 -0400
do not count indel with "view -Y"
commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jul 7 00:35:25 2011 -0400
for WIN32 compatibility
commit 70a52501bcfa63824749893a5ab8ed3c38e34958
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jul 7 00:32:46 2011 -0400
for WIN32 compatibility
commit 00438f14ed5984f08e8f7645a9b95644a812f969
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jul 6 23:41:45 2011 -0400
fixed an uninitialized variable
commit 7609c4a01059c326544b3d0142dfe9c4229d68c6
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jul 6 23:39:31 2011 -0400
fixed an uninitialized variable
commit cec7189a412f80ccb068a73bd28528915c16b0bf
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jul 6 22:53:19 2011 -0400
Release samtools-0.1.17
commit 93c06a249de3bb666029bf07b66de5e8e5e314fa
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jul 6 09:46:09 2011 -0400
bugfix: incorrect idxstats for the last seq
Again, this bug is caused by 3rd-party code for the sorting order checking.
commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jul 5 23:30:23 2011 -0400
output mapping quality in the old pileup format
commit 362e05fd670886acaede69b864903d730b9db3ca
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jul 5 21:59:22 2011 -0400
added a brief description of the VCF format
commit e690a696468205e0cc4560016361c997660dd496
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jul 5 16:23:10 2011 -0400
improved samtools manual page
commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jul 5 15:58:29 2011 -0400
merge bcftools.1 to samtools.1
commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a
Author: Heng Li <lh3@live.co.uk>
Date: Tue Jul 5 13:39:02 2011 -0400
mpileup: when region set, set reference properly
commit 613e4d67624a94f62563935fbd5cc294df69605a
Author: Heng Li <lh3@live.co.uk>
Date: Mon Jul 4 23:29:02 2011 -0400
compute the min PL diff
commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53
Author: Heng Li <lh3@live.co.uk>
Date: Mon Jul 4 22:57:48 2011 -0400
rename trio.c to mut.c
commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc
Author: Heng Li <lh3@live.co.uk>
Date: Sun Jul 3 15:38:51 2011 -0400
added pair caller interface; not tested
commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c
Author: Heng Li <lh3@live.co.uk>
Date: Sun Jul 3 15:24:23 2011 -0400
inital implementation of a pair caller
commit e97653cf2ad653c95886933c42a2b5492ccab5ff
Author: Heng Li <lh3@live.co.uk>
Date: Sun Jul 3 00:06:28 2011 -0400
convert bam to single-end fastq
commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd
Author: Heng Li <lh3@live.co.uk>
Date: Sat Jul 2 14:39:18 2011 -0400
improve BED parsing
commit 1025714325fdc636aeee47a76db8dafbbbfde64b
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 1 14:19:54 2011 -0400
update the manual page
commit 8022d0039dff47b1c11b2421357d510c1f28ae15
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 1 14:17:03 2011 -0400
output the best constrained genotypes in trio
commit 18c87295e12f5bebafdcae00d52000fb94c8a566
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jul 1 11:18:14 2011 -0400
added documentations for view -T
commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 22:45:20 2011 -0400
fixed a bug in writing SP
commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 22:35:25 2011 -0400
optionally output read positions in mpileup
commit 1008051155ec994c1901e18f3eb03ea32a62e5d7
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 22:17:25 2011 -0400
make faidx works with <2GB lines
commit 2daebb63762425dd3074ddf71582ad189001e394
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 17:28:58 2011 -0400
fixed an issue in the trio caller and the indel caller
commit 9fdd52cf0716fb342a94946433d564b28b230835
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 13:34:01 2011 -0400
Added trio caller; NOT tested yet
commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 11:42:29 2011 -0400
convert PL to 10-likelihood GL
commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d
Author: Heng Li <lh3@live.co.uk>
Date: Thu Jun 30 10:49:05 2011 -0400
fix a compatibility issue with the new bcftools
commit d340f01f609c61b719d38a6a55629a3fc899e1cd
Author: Heng Li <lh3@live.co.uk>
Date: Sun Jun 26 23:41:20 2011 -0400
allow to ignore RG
commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542
Author: Heng Li <lh3@live.co.uk>
Date: Sun Jun 5 23:05:21 2011 -0400
fixed a bug in SO checking due to a recent change
commit bc995abf666d0c9ab4258f6c1b3518a45a89209f
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jun 3 14:45:36 2011 -0400
update the version number
commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c
Author: Heng Li <lh3@live.co.uk>
Date: Fri Jun 3 14:43:12 2011 -0400
smarter way to parse a region string
commit e58a90a0fde54053dac65352b34c13c3fea815fc
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 14:36:22 2011 -0400
output LRT2 instead of LRT1
commit 08f78c9af3e5661f04f80bef424232de721dba03
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 14:02:28 2011 -0400
genotype test, but assuming 1-degree
commit 587b852340d7e60f6f7cf474a92ef77aeab46018
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 12:55:19 2011 -0400
perform 2-degree test by default
commit 3d38e403c5c830478b7eb157a484776997440501
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 12:44:34 2011 -0400
fixed a typo; but the result is still not good
commit 06291624f7dcc57445676f3be25d0bc355dd7110
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 12:24:18 2011 -0400
fixed a typo
commit 63b98aa33636b0d82a435bf49153c8c1502e7d42
Author: Heng Li <lh3@live.co.uk>
Date: Wed Jun 1 12:23:37 2011 -0400
added HWE+F<0 filter
commit 37d926e8999999b593d0637ab7dc379dbd3d6006
Author: Heng Li <lh3@live.co.uk>
Date: Wed May 4 10:11:59 2011 -0400
improved sorting order checking in index
Patches from Jonathan Manning
commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf
Author: Heng Li <lh3@live.co.uk>
Date: Tue May 3 23:09:05 2011 -0400
added r^2 estimate; added Brent's method
commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75
Author: Heng Li <lh3@live.co.uk>
Date: Sun May 1 23:45:23 2011 -0400
combine several utilites into vcfutils.lua
commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 27 21:09:22 2011 -0400
minor warning
commit 683ef0443860813d743cf84fa86dda9bfaf5445a
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 27 10:10:38 2011 -0400
added versioning
commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 27 10:04:02 2011 -0400
Output ML allele count
commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000
Author: Heng Li <lh3@live.co.uk>
Date: Tue Apr 26 16:14:20 2011 -0400
use ar -s
commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949
Author: Heng Li <lh3@live.co.uk>
Date: Sat Apr 23 01:22:31 2011 -0400
added another type of LRT
commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 22 16:00:31 2011 -0400
added version
commit 8fad6677c5952efd67391581d64e67e02e7f6e68
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 22 00:30:19 2011 -0400
remove the pileup command
commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 21 23:10:45 2011 -0400
Release 0.1.16 (r963:234)
commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 21 12:44:44 2011 -0400
fixed a bug when coordinate-less reads are on the reverse strand
commit c5ec45a128f409debc6a56a798024f53004037dc
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 20 11:36:52 2011 -0400
added option '-f' to merge to avoid overwritting
commit 68d431531370d24907c01a27f166f2341d7c4d35
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 20 10:26:58 2011 -0400
do not print a warning
commit 32922607e51ad2260c337eb022b9e4aedacb049f
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 20 10:21:06 2011 -0400
Added ldpair to compute LD between requested pairs
commit b8d6fa71b91678fa02338257e0707d1e5ca098dd
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 17 21:51:43 2011 -0400
On a toy sample, type "B" seems to be accepted
commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 17 21:21:20 2011 -0400
added type "B"; not tested yet
commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 17 19:25:54 2011 -0400
fixed a bug in bedidx.c: input BED not sorted
commit de1e192bb0a8a762a54a6eee81d882fab01c3d32
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 17 18:51:08 2011 -0400
by default, always perform posterior chi^2
commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35
Author: Heng Li <lh3@live.co.uk>
Date: Sat Apr 16 12:33:28 2011 -0400
added debugging
commit 8ce52e024dc2ef361dbd5399c232163055057e70
Author: Heng Li <lh3@live.co.uk>
Date: Sat Apr 16 00:59:05 2011 -0400
avoid a segfault given wrong input
commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 19:55:39 2011 -0400
do not segfault when there is no PL
commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 11:59:55 2011 -0400
remove another unused part
commit f53a051d68bf312ac8d5865210fae7a9808c0fb9
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 10:41:25 2011 -0400
print G3 if HWE is small
commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 10:04:34 2011 -0400
fixed a bug
actually not fix, but hide it
commit 088e13c32453fb533b7bb1c65a573f9b90a23625
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 09:48:47 2011 -0400
added LRT based permutation; not used though
commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 09:28:55 2011 -0400
Perform posterior contrast for small LRT
Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is
more robust to sequencing artifacts. Thus we may combine the two to achieve a
balance between speed and low FPR.
commit 6f1b066270902198a7175ff6c1b05ebc8d1919be
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 15 01:36:06 2011 -0400
Added Brent's method
commit 3d061e5db25b67b25f6ff87afe4162e121354232
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 23:30:10 2011 -0400
fixed a typo in printing
commit 7fd14ceb5990bb350b8e97346ef3537d80058def
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 23:14:23 2011 -0400
fixed a stupid bug
commit f5b2c3459ec098b3cafd9619b9077132516baf58
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 22:42:35 2011 -0400
separate EM and posterior
Now, constrast is not performed unless -C is in use. EM can be invoked
independently with -e without computing the posterior.
commit 9eefcac963697fae554789b11ae3cb2c23f224d0
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 22:00:19 2011 -0400
further code cleanup; prepare to add EM interface
commit c2cce52355262743711e4742b0c8542bfcab1cdd
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 21:44:03 2011 -0400
drop EM from prob1
commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 21:08:33 2011 -0400
drop posterior LRT; prepare for clean up
commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 20:57:43 2011 -0400
better initial values for LD
commit d48a8873c060b18b57799cfe3a0e5496ba069457
Author: Heng Li <lh3@live.co.uk>
Date: Thu Apr 14 20:36:25 2011 -0400
finished EM
commit b101f2db476188a950c23f5c1b6185fdb7f8f40b
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 13 01:19:04 2011 -0400
genotype frequency estimate
commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 13 00:37:22 2011 -0400
prepare for code clean up
commit e0ce416abfc094f0c090957080b1404fd0edf752
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 13 00:34:15 2011 -0400
rename ld.c to em.c
commit 45ede3ad181f35c1be24bed5d75841e472357ab7
Author: Heng Li <lh3@live.co.uk>
Date: Wed Apr 13 00:22:10 2011 -0400
implemeted EM likelihood ratio test
The idea is learned from a brief chat with Rasmus Nielsen.
commit 0454a346b60e42b75a2f742272089810279c7131
Author: Heng Li <lh3@live.co.uk>
Date: Tue Apr 12 15:45:52 2011 -0400
added likelihood-ratio test (idea from Nick)
commit f6287c8646c690440a1554c8958e7268f4134dc2
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 10 18:24:37 2011 -0400
Release samtools-0.1.15 (r949:203)
commit de6023f38f4d652438557cf7a0ac6eec324e7416
Author: Heng Li <lh3@live.co.uk>
Date: Sun Apr 10 15:54:58 2011 -0400
improved help information
commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279
Author: Heng Li <lh3@live.co.uk>
Date: Sat Apr 9 16:28:01 2011 -0400
fixed a minor issue
commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235
Author: Heng Li <lh3@live.co.uk>
Date: Sat Apr 9 15:49:04 2011 -0400
separate QC-pass and QC-fail reads
commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 8 17:45:19 2011 -0400
added verbose level
commit f7bf419c290462be7d289249a4a6d28f825b4c93
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 8 16:08:14 2011 -0400
fixed a bug
commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 8 16:00:37 2011 -0400
drop unrelated @RG when "-R" is in use
commit a62dc929c950fb51311b705f5b5bfba8e3f704d7
Author: Heng Li <lh3@live.co.uk>
Date: Fri Apr 8 16:00:14 2011 -0400
skip header validation
commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9
Author: Heng Li <lh3@live.co.uk>
Date: Tue Apr 5 23:52:22 2011 -0400
change error message
commit c0c50a34df250ef8a7a29b172058cd229be582b5
Author: Heng Li <lh3@live.co.uk>
Date: Tue Apr 5 23:50:46 2011 -0400
fixed a bug caused by recent modifications
commit 25226e8c468404cb5e1b5272efcea57e4193c762
Author: Heng Li <lh3@live.co.uk>
Date: Tue Apr 5 13:31:19 2011 -0400
reduce the indel filtering window
commit 5e18d7014437734f9dac9ab45a95e43ec2526101
Author: Heng Li <lh3@live.co.uk>
Date: Mon Apr 4 13:56:20 2011 -0400
only output hwe if it is small enough
commit 614941fb7dd276de662e7820eb8c7bae871a18cc
Author: Heng Li <lh3@live.co.uk>
Date: Mon Apr 4 13:34:02 2011 -0400
added HWE back
commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d
Author: Heng Li <lh3@live.co.uk>
Date: Mon Apr 4 12:46:24 2011 -0400
EM estimate of genotype frequency
commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3
Author: Heng Li <lh3@live.co.uk>
Date: Mon Apr 4 11:29:12 2011 -0400
minor
commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b
Author: Heng Li <lh3@live.co.uk>
Date: Mon Apr 4 11:24:04 2011 -0400