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https://github.com/pysam-developers/pysam
24 July 2024, 06:47:36 UTC
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Revision Author Date Message Commit Date
3644505 Andreas Heger 10 January 2019, 22:35:44 UTC Merge pull request #751 from nsoranzo/remove_sudo_false Remove deprecated sudo: false from .travis.yml 10 January 2019, 22:35:44 UTC
2d30332 Andreas Heger 10 January 2019, 22:21:25 UTC {AH} update release notes 10 January 2019, 22:21:25 UTC
a087d71 Andreas Heger 10 January 2019, 21:54:11 UTC {AH} catch pileup itorator out-of-scope segfaults, closes #746 10 January 2019, 21:54:11 UTC
bfe3c73 Nicola Soranzo 10 January 2019, 13:02:25 UTC Remove deprecated sudo: false from .travis.yml See https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migration 10 January 2019, 13:02:29 UTC
01e6e64 Andreas Heger 09 January 2019, 22:40:17 UTC Merge pull request #750 from pysam-developers/AH-fix-faidx-fetch-with-region {AH} fix faixd fetch with region, closes #747 09 January 2019, 22:40:17 UTC
a3e3b9c Andreas Heger 09 January 2019, 22:37:35 UTC {AH} update test case for aligned_ref, see issue #737 09 January 2019, 22:37:35 UTC
d893045 Andreas Heger 09 January 2019, 22:26:25 UTC Merge branch 'bkohrn-master' 09 January 2019, 22:26:25 UTC
84e2a05 Andreas Heger 09 January 2019, 22:26:08 UTC {AH} add test case for aligned_ref, see issue #737 09 January 2019, 22:26:08 UTC
1264d01 Andreas Heger 09 January 2019, 22:09:38 UTC Merge branch 'master' of https://github.com/bkohrn/pysam into bkohrn-master 09 January 2019, 22:09:38 UTC
02798c8 Andreas Heger 09 January 2019, 21:52:52 UTC {AH} fix faixd fetch with region, closes #747 09 January 2019, 21:52:52 UTC
4262794 Andreas Heger 08 January 2019, 21:09:57 UTC Merge pull request #748 from pysam-developers/AH-increaseMaxPos Ah increase max pos 08 January 2019, 21:09:57 UTC
1119c82 Andreas Heger 07 January 2019, 20:46:52 UTC {AH} disable test for faidx:ftp 07 January 2019, 20:46:52 UTC
b303daf Andreas Heger 05 January 2019, 21:28:18 UTC {AH} disable test for faidx:ftp 05 January 2019, 21:28:18 UTC
a1b5cef Andreas Heger 02 January 2019, 22:33:56 UTC {AH} set MAX_POS to (1 << 31) - 1, fixes #741 and #732 02 January 2019, 22:33:56 UTC
fc3f522 Andreas Heger 09 December 2018, 22:25:32 UTC {AH} increase max position to 2 << 31, fixes #732 09 December 2018, 22:25:32 UTC
155f61e Andreas Heger 09 December 2018, 22:21:54 UTC Revert "{AH} increase max position to 2 << 31, fixes #732" This reverts commit d6152e9db6ec861073bafccea5e4203dccec7b54. 09 December 2018, 22:21:54 UTC
d6152e9 Andreas Heger 08 December 2018, 20:53:57 UTC {AH} increase max position to 2 << 31, fixes #732 08 December 2018, 20:53:57 UTC
807863b Andreas Heger 08 December 2018, 20:50:44 UTC {AH} increase version to 0.15.2 08 December 2018, 20:50:44 UTC
8a4e9d1 Andreas Heger 05 December 2018, 21:14:50 UTC Merge pull request #729 from SoapZA/fix-missing-lzma_stub.h Add missing macOS stub files in `MANIFEST.in` 05 December 2018, 21:14:50 UTC
ed856a3 bkohrn 26 October 2018, 23:18:40 UTC Fix bug in get_aligned_pairs I noticed that in pysam 0.15.1, there is a bug with the get_aligned_pairs function when matches_only=True and with_seq=True. Basically, the read position gets advanced, but the reference position does not. This fixes that bug, and I believe it won't involve changing any other portions of the code. 26 October 2018, 23:18:40 UTC
5b00a3c David Seifert 30 September 2018, 17:23:14 UTC Add missing macOS stub files in `MANIFEST.in` * This caused the PyPI tarballs to miss the stubs required for building htslib on macOS. This would not show up for source-tree builds, as the files are included in git, just not in `MANIFEST.in`. Fixes #645 30 September 2018, 17:23:14 UTC
e4b34cd Andreas Heger 28 September 2018, 19:54:54 UTC {AH} fix double declaration 28 September 2018, 19:54:54 UTC
a9cec68 Andreas Heger 28 September 2018, 19:36:13 UTC {AH} remove deprecated tostring method 28 September 2018, 19:36:13 UTC
956e9c1 Andreas Heger 28 September 2018, 15:50:20 UTC {AH} remove deprecated tostring method 28 September 2018, 15:50:20 UTC
86694a4 Andreas Heger 13 September 2018, 20:31:13 UTC {AH} increase version to 0.15.1 13 September 2018, 20:31:13 UTC
c75e575 Andreas Heger 13 September 2018, 20:15:05 UTC {AH} clear up release.rst, update news for v0.15.1 release 13 September 2018, 20:15:05 UTC
4b05211 Andreas Heger 13 September 2018, 20:12:00 UTC {AH} remove bcftools/config.h, fixes #714 13 September 2018, 20:12:00 UTC
dc19785 Andreas Heger 13 September 2018, 20:10:43 UTC {AH} raise ValueError if tid is out of range when writing record, fixes #716 13 September 2018, 20:10:43 UTC
a89515a Andreas Heger 11 September 2018, 20:48:35 UTC {AH} ignore samtools idxstats usage test 11 September 2018, 20:48:35 UTC
671d9fa Andreas Heger 11 September 2018, 19:29:18 UTC Merge pull request #715 from smoe/patch-1 pysam_data: cleaning of generated with_md.sam.gz 11 September 2018, 19:29:18 UTC
09a43cd Andreas Heger 11 September 2018, 19:28:33 UTC Merge pull request #712 from kyleabeauchamp/master Update NEWS for 0.15.0 release 11 September 2018, 19:28:33 UTC
6df997d Andreas Heger 11 September 2018, 19:28:18 UTC Merge branch 'master' into master 11 September 2018, 19:28:18 UTC
5fe7b3f Steffen Möller 29 July 2018, 17:25:24 UTC pysam_data: cleaning of generated with_md.sam.gz 29 July 2018, 17:25:24 UTC
9d83174 Andreas Heger 28 July 2018, 19:49:51 UTC {AH} fix typo in test, update NEWS and release.rst for release 28 July 2018, 19:49:51 UTC
0720fbf Andreas Heger 27 July 2018, 21:12:40 UTC {AH} return None in get_forward_sequence if sequence not defined, fixes #658 27 July 2018, 21:12:40 UTC
11b373a Andreas Heger 27 July 2018, 20:29:21 UTC {AH} allow dash in chromosome names of region string, fixes #673 27 July 2018, 20:29:21 UTC
0b77c59 Andreas Heger 26 July 2018, 21:39:34 UTC {AH} permit lowercase md tag, fixes #683 26 July 2018, 21:39:34 UTC
48840ca Kyle Beauchamp 26 July 2018, 20:27:19 UTC Update NEWS for 0.15.0 release 26 July 2018, 20:27:19 UTC
bca66ee Andreas Heger 26 July 2018, 20:04:24 UTC Merge pull request #707 from kyleabeauchamp/puts_kab Fix EOF issue, part 3 26 July 2018, 20:04:24 UTC
c3c98a1 Andreas Heger 26 July 2018, 20:03:24 UTC Merge pull request #708 from kyleabeauchamp/delsave Remove save directory 26 July 2018, 20:03:24 UTC
aab8555 Andreas Heger 26 July 2018, 20:02:50 UTC Merge pull request #709 from kyleabeauchamp/delbench Delete benchmark directory 26 July 2018, 20:02:50 UTC
0993d1b Andreas Heger 26 July 2018, 20:02:13 UTC Merge pull request #711 from kyleabeauchamp/docs Clean up README 26 July 2018, 20:02:13 UTC
f0d464f Andreas Heger 26 July 2018, 19:57:58 UTC {AH} add HTSFile to docs for parse_region, see #700 26 July 2018, 19:57:58 UTC
ebefe41 Kyle Beauchamp 26 July 2018, 03:40:19 UTC Clean up README 26 July 2018, 03:40:19 UTC
577cc41 Kyle Beauchamp 25 July 2018, 22:25:38 UTC Delete benchmark directory 25 July 2018, 22:25:38 UTC
617b2a2 Kyle Beauchamp 25 July 2018, 22:13:22 UTC Remove save directory 25 July 2018, 22:13:22 UTC
f548884 Kyle Beauchamp 25 July 2018, 15:02:59 UTC Apply patches 25 July 2018, 15:02:59 UTC
184f1d9 John Marshall 25 July 2018, 09:41:46 UTC Add @pysam@_puts() wrapper function Rather than trying to rewrite a function call as two function calls when we don't really know what the syntax around the call site looks like, rewrite it as a call to our own function. Fixes #646. 25 July 2018, 09:48:02 UTC
c985acc Andreas Heger 23 July 2018, 20:06:38 UTC Merge pull request #656 from nh13/patch-2 Support `text` when opening a SAM file for writing 23 July 2018, 20:06:38 UTC
0f16708 Andreas Heger 23 July 2018, 20:04:13 UTC Merge pull request #662 from kyleabeauchamp/cleanup2 Move lots of stuff from top-level dir to /devtools 23 July 2018, 20:04:13 UTC
68e307a Andreas Heger 23 July 2018, 20:01:24 UTC Merge pull request #701 from kyleabeauchamp/hts19 [WIP] Upgrade pysam to use htslib, samtools, and bcftools 1.9 23 July 2018, 20:01:24 UTC
d94d581 Andreas Heger 22 July 2018, 21:14:03 UTC {AH{ remove .tmp filee 22 July 2018, 21:14:18 UTC
ef3f05e Andreas Heger 22 July 2018, 21:13:16 UTC {AH} disable CRAM test - issue with reference sequerce 22 July 2018, 21:14:17 UTC
1961327 Andreas Heger 22 July 2018, 21:12:44 UTC {AH} use API call to set CRAM Reference sequence 22 July 2018, 21:14:17 UTC
3ce4d2c Kyle Beauchamp 18 July 2018, 20:32:08 UTC Update pysam version 22 July 2018, 21:14:17 UTC
fadbafb Kyle Beauchamp 18 July 2018, 20:31:55 UTC Update samtools, bcftools, and htslib vendored files 22 July 2018, 21:14:17 UTC
48111f5 Kyle Beauchamp 18 July 2018, 20:32:08 UTC Update pysam version 18 July 2018, 20:32:08 UTC
acaadce Kyle Beauchamp 18 July 2018, 20:31:55 UTC Update samtools, bcftools, and htslib vendored files 18 July 2018, 20:31:55 UTC
24c0f2f Andreas Heger 02 July 2018, 20:52:22 UTC Merge pull request #694 from dpryan79/get_blocks_CIGAR Ensure that = and X CIGAR ops are treated the same as M 02 July 2018, 20:52:22 UTC
c0685a1 Devon Ryan 02 July 2018, 18:49:29 UTC Ensure that = and X CIGAR ops are treated the same as M 02 July 2018, 18:49:29 UTC
aa27e81 Marius van den Beek 11 May 2018, 11:18:49 UTC Allow setting number of threads for htslib (#638) * Allow setting number of threads for htslib Internally this uses hts_set_threads. There is only a minor speedup for reading files, but writing files can benefit well from setting n_threads to more than 1: ``` In [1]: def benchmark_write(threads=1): ...: source = pysam.AlignmentFile('/Users/mvandenb/src/readtagger/tests/h4.bam', threads=threads) ...: out = pysam.AlignmentFile('out.bam', mode='wb', template=source, threads=threads) ...: for _ in range(1000000): ...: out.write(next(source)) ...: In [2]: %timeit benchmark_write(threads=1) 1 loop, best of 3: 9.21 s per loop In [3]: %timeit benchmark_write(threads=2) 1 loop, best of 3: 4.68 s per loop In [4]: %timeit benchmark_write(threads=3) 1 loop, best of 3: 3.17 s per loop In [5]: %timeit benchmark_write(threads=4) 1 loop, best of 3: 2.66 s per loop ``` This had been discussed in https://github.com/pysam-developers/pysam/issues/579#issuecomment-370766946. * Avoid combining n_threads > 1 w/ ignore_truncation Apparently htslib won't raise a separate error if hitting a truncated read. Also subtracts 1 from `n_threads`, since `hts_set_threads` will add additional threads. This should be more intuitive to users. Also moves `hts_set_threads` as the last action when cerating new AlignmentFile instances. * Rename `n_thread` to `thread` * Move hts_set_threads to HTSFile class * Implement threads for pysam.VariantFile * Implement threads for pysam.TabixFile 11 May 2018, 11:18:49 UTC
9a062fe Kyle Beauchamp 07 April 2018, 19:58:28 UTC Fix path 07 April 2018, 19:58:28 UTC
42236a1 Kyle Beauchamp 07 April 2018, 19:56:50 UTC Move lots of stuff from top-level dir to /devtools 07 April 2018, 19:56:50 UTC
66ed24e Nils Homer 04 April 2018, 22:17:38 UTC Support `text` when opening a SAM file for writing 04 April 2018, 22:17:38 UTC
09fb70e Andreas Heger 20 March 2018, 22:07:49 UTC {AH} update NEWS 20 March 2018, 22:07:49 UTC
7077972 Andreas Heger 20 March 2018, 22:02:59 UTC {AH} add bcftools 1.7 20 March 2018, 22:02:59 UTC
96edc75 Andreas Heger 20 March 2018, 21:46:30 UTC {AH} double check remote data tests 20 March 2018, 21:46:30 UTC
f164517 Andreas Heger 20 March 2018, 21:29:29 UTC {AH} update release notes for v0.14.1 20 March 2018, 21:29:29 UTC
ad9c0ab Andreas Heger 17 March 2018, 20:33:49 UTC Merge pull request #621 from wckdouglas/master Adding a warning to count_coverage when an alignment has an empty QUAL field 17 March 2018, 20:33:49 UTC
b4adaff Andreas Heger 17 March 2018, 20:30:43 UTC Merge pull request #635 from wckdouglas/speed_up_find_intron Speed up find intron 17 March 2018, 20:30:43 UTC
9b2466b Andreas Heger 17 March 2018, 20:23:18 UTC {AH} remove unsued imports 17 March 2018, 20:23:18 UTC
12e0701 Andreas Heger 16 March 2018, 15:23:05 UTC {AH} treat border case of all bases in pileup column below quality score 16 March 2018, 15:29:49 UTC
6b345a3 Andreas Heger 16 March 2018, 15:20:17 UTC {AH} fix header access in pileup column 16 March 2018, 15:20:17 UTC
34ba3fc Douglas Wu 02 March 2018, 23:20:59 UTC modified comment 02 March 2018, 23:20:59 UTC
1a76af1 Douglas Wu 02 March 2018, 20:56:42 UTC uses set comparison 02 March 2018, 20:56:42 UTC
b2d32bc Douglas Wu 02 March 2018, 19:21:48 UTC cythonize alignment 02 March 2018, 19:21:48 UTC
c0fbdeb Douglas Wu 02 March 2018, 18:23:02 UTC removed redundant assignment 02 March 2018, 18:23:02 UTC
5e46d48 Douglas Wu 02 March 2018, 18:13:14 UTC uses cdef types according to get_aligned_pairs for find_introns 02 March 2018, 18:13:14 UTC
7c605ac Douglas Wu 02 March 2018, 17:49:16 UTC uses added comments for find_introns 02 March 2018, 17:49:16 UTC
c56b0d1 Douglas Wu 02 March 2018, 17:00:13 UTC uses r.cigartuples for find_introns 02 March 2018, 17:00:13 UTC
50d6895 Douglas Wu 02 March 2018, 16:36:36 UTC added faster function for find_introns 02 March 2018, 16:36:36 UTC
b7ae8f1 Douglas Wu 01 March 2018, 16:34:36 UTC fixed pos bug 01 March 2018, 16:34:36 UTC
e6f18a8 Douglas Wu 01 March 2018, 07:38:45 UTC speed up intron 01 March 2018, 07:38:45 UTC
76bec77 Andreas Heger 12 February 2018, 20:41:57 UTC {AH} add missing test data, fixes #622 12 February 2018, 20:41:57 UTC
6426804 wckdouglas 12 February 2018, 18:17:09 UTC base qual filter using >= to match previous behaviour 12 February 2018, 18:17:09 UTC
5d45203 wckdouglas 12 February 2018, 17:57:50 UTC fixed wrong base qual comparison 12 February 2018, 17:57:50 UTC
f89911f Douglas Wu 12 February 2018, 17:53:39 UTC fixed if-clause for check base qual 12 February 2018, 17:53:39 UTC
c5d9a13 Douglas Wu 12 February 2018, 17:48:53 UTC fixed 12 February 2018, 17:48:53 UTC
5715b7c wckdouglas 12 February 2018, 17:46:06 UTC fixed quality check, skip if null quality and quality_threshold == 0 or None 12 February 2018, 17:46:06 UTC
ce895a1 wckdouglas 12 February 2018, 15:49:45 UTC fixed empty QUAL, removed warning and used quality threshold to control the behaviour 12 February 2018, 15:49:45 UTC
ac02694 wckdouglas 12 February 2018, 15:40:24 UTC fixed empty QUAL, removed warning and used quality threshold to control the behaviour 12 February 2018, 15:40:24 UTC
94924f7 Douglas Wu 12 February 2018, 05:11:31 UTC fixed warning 12 February 2018, 05:11:31 UTC
6fcee40 Douglas Wu 12 February 2018, 04:58:18 UTC reset quality thershold flag 12 February 2018, 04:58:18 UTC
505f627 Douglas Wu 12 February 2018, 04:49:08 UTC reset setup.py 12 February 2018, 04:49:08 UTC
57b72b1 wckdouglas 12 February 2018, 04:11:59 UTC added warning to NULL quality alignments in count_coverage 12 February 2018, 04:11:59 UTC
c8878a8 Douglas Wu 12 February 2018, 01:04:15 UTC modified 12 February 2018, 01:04:15 UTC
af6ff23 Andreas Heger 09 February 2018, 21:48:27 UTC Merge pull request #620 from pysam-developers/AH-add_alignmentfileheader_dict_methods {AH} add backwards compatibility functions for AlignmentHeader, fixes… 09 February 2018, 21:48:27 UTC
b7ce5e6 Andreas Heger 09 February 2018, 21:22:11 UTC {AH} sort for py2.7 in header comparison 09 February 2018, 21:22:11 UTC
d84ba01 Andreas Heger 09 February 2018, 21:01:32 UTC {AH} fix typo 09 February 2018, 21:01:32 UTC
f55c453 Andreas Heger 09 February 2018, 20:34:18 UTC {AH} update release notes and versions, fixes #619 09 February 2018, 20:34:18 UTC
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