Branch: master

bio2

georgeg

master

sambamba

segfaults

v0.1

v0.1.0

v0.2.0

v0.2.1

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421 Commits (master)

 

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Author	SHA1	Message	Date
John Colvin	27cbaadf37	better .travis.yml, uses dub test and tests ldc	6 years ago
John Colvin	0ec8d39d8f	fix tabs/spaces in dub.json	6 years ago
John Colvin	05f86b8877	fix toHash signature	6 years ago
John Colvin	4394f15bfd	fix deprecations and some warnings	6 years ago
John Colvin	4901cda765	std.c -> core.stdc	6 years ago
John Colvin	c37b0e7e03	switch to undead.stream;	6 years ago
Artem Tarasov	1248586b54	fixes lomereiter/sambamba#244	6 years ago
George Githinji	95c8167116	Merge remote-tracking branch 'upstream/master' * upstream/master: use consistent naming (#21) + include the AH header tag to @SQ lines improved big endian support travis badge fix travis.yml fix licensing confusion add travis.yml for Continuous Integration Add dub config file	6 years ago
George Githinji	1af61448a9	added a fastq parser	6 years ago
Artem Tarasov	47d081e06c	use consistent naming (#21)	6 years ago
Artem Tarasov	89664db077	Merge pull request #21 from indraniel/sq-ah-header-tag + include the AH header tag to @SQ lines	6 years ago
indraniel	589d65025a	+ include the AH header tag to @SQ lines - the "AH" header tag corresponds to Alternate Haplotypes in ALT mapping mode - based on samtools/hts-specs issue 147: https://github.com/samtools/hts-specs/pull/147 - this tag is already being produced by `bwa` 0.7.15 * see tag 0.7.15 (r1140) https://github.com/lh3/bwa/releases/tag/v0.7.15	6 years ago
Artem Tarasov	0b44f2a93e	improved big endian support	6 years ago
Artem Tarasov	59d0c2bdb7	travis badge	6 years ago
Artem Tarasov	8a18c41b19	fix travis.yml	6 years ago
Artem Tarasov	aea2c02c39	fix licensing confusion	6 years ago
Artem Tarasov	834fd27e9e	Merge pull request #20 from wilzbach/add_dub Add dub & travis CI config files	6 years ago
Sebastian Wilzbach	e16843cedd	add travis.yml for Continuous Integration	6 years ago
Sebastian Wilzbach	cb60c3ec6b	Add dub config file	6 years ago
Artem Tarasov	ea60623c05	import fix	6 years ago
Artem Tarasov	3e73b672b8	fix initializing new reference in pileup a read aligned to next reference can have the same position and be included into the column	6 years ago
Artem Tarasov	84fd950575	whitespace fix	6 years ago
Artem Tarasov	bf564a9064	lowering memory footprint for huge headers	6 years ago
Artem Tarasov	59cdeb650c	minimize MultiBamReader overhead for a single file	6 years ago
Artem Tarasov	6622e8dfac	added .ref_name and .mate_ref_name to BamRead	6 years ago
Artem Tarasov	faa3cab19e	fix 32-bit compilation	6 years ago
Artem Tarasov	7efdb8a2f7	on-the-fly indexing: handle multi-block reads	7 years ago
Artem Tarasov	1eb4a6761e	BamWriter: always recalculate the bin of reads	7 years ago
Artem Tarasov	e992a27e4a	Merge pull request #16 from biorelated/master rename examples; fix indentation	7 years ago
biorelated	29b36a225c	fix indetation;rename file	7 years ago
biorelated	1f22a2591f	fix indentation; rename example file	7 years ago
biorelated	20ddf4ba1f	fix indentation; rename to reflect function of the example	7 years ago
biorelated	00b3574da1	rename example3	7 years ago
biorelated	ba6172dc49	rename example2 to print_base_info. fix indentation	7 years ago
biorelated	909ba7b05d	Merge remote-tracking branch 'upstream/master' * upstream/master: fix #12	7 years ago
Artem Tarasov	9b5838fe25	fix #12 commented out a static assert that DMD somehow miscompiles; updated example5.d (no longer works correctly with nWayUnion, plus there's the multireader available, which is better anyway)	7 years ago
biorelated	982c4f670f	Merge remote-tracking branch 'upstream/master' * upstream/master: reference access to header records (fixes #14) readsWithProgress: ensure finishFunc is called only once MultiBamReader: added readsWithProgress method throw write errors 2.067 fixes fixes for 2.067 frontend	7 years ago
Artem Tarasov	842f0ab549	reference access to header records (fixes #14)	7 years ago
Artem Tarasov	0366a254d9	readsWithProgress: ensure finishFunc is called only once	7 years ago
Artem Tarasov	f246c5c993	MultiBamReader: added readsWithProgress method	7 years ago
Artem Tarasov	13721d7ca0	throw write errors	7 years ago
Artem Tarasov	57e73f2b31	2.067 fixes	7 years ago
biorelated	1d4ec479ab	update with upstream commit to skip unmapped chunks Merge branch 'master' of https://github.com/biod/BioD * 'master' of https://github.com/biod/BioD: pileupChunks: skip unmapped chunks set BGZF block start offset when the input is pipe	7 years ago
Artem Tarasov	d54f90fb68	fixes for 2.067 frontend	7 years ago
Artem Tarasov	0e924443aa	pileupChunks: skip unmapped chunks	7 years ago
Artem Tarasov	17cee6fd30	set BGZF block start offset when the input is pipe fixes lomereiter/sambamba#144	7 years ago
biorelated	9cd1d2974e	fix typo in comment	7 years ago
Artem Tarasov	93ac39e25b	fix compression buffer size	7 years ago
Artem Tarasov	30773ec5a2	mixed string comparison (lomereiter/sambamba#109)	7 years ago
Artem Tarasov	2b0f64a25a	Merge pull request #11 from georgeG/master Changes to the README	7 years ago