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bio2

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sambamba

segfaults

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427 Commits (segfaults)

 

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Author	SHA1	Message	Date
Pjotr Prins	c865ee2de2	Compilation fixes for ldc 1.11	4 years ago
Pjotr Prins	dd07f34979	Fixes: BioD/bio/maf/reader.d(53): Error: cannot implicitly convert expression `this._f.byLine(cast(Flag)true, '\x0a')` of type `ByLineImpl!(char, char)` to `ByLine!(char, char)` See https://github.com/bioconda/bioconda-recipes/pull/8787#issuecomment-389195848	4 years ago
George	3513df92a6	update github account link	4 years ago
Pjotr Prins	8527852a38	README	4 years ago
Pjotr Prins	f4a6c1c55c	Introducing my recent D-style rewrite of bamreader. This version is still single threaded (there is room for pre-fetching blocks), but proves very fast and lazy. The original working commits can be found on this branch https://github.com/pjotrp/sambamba/tree/markdup2	4 years ago
Pjotr Prins	a84bbed78f	Merge branch 'master' of github.com:pjotrp/BioD	4 years ago
Pjotr Prins	5e56b2bb45	Merge branch 'master' of github.com:biod/BioD	5 years ago
Pjotr Prins	45668d48a5	asserte amendments	5 years ago
Pjotr Prins	79fa83784d	Added 'asserte' method which throws an exception on assert (failure). Standard assert does not throw exceptions which can make it hard to locate problems. And enforce still works in release versions. This is the middle ground.	5 years ago
Pjotr Prins	6bb0156553	Merge pull request #35 from biorelated/master fix deprecation warnings: integral promotion not done	5 years ago
George Githinji	8d0694f864	fix deprecation warnings: integral promotion not done	5 years ago
Pjotr Prins	d31400bc40	Merge pull request #34 from biorelated/master update the instructions for running the example code	5 years ago
George Githinji	ffd9cfd179	resetting Merge branch 'master' of biorelated:biorelated/BioD * 'master' of biorelated:biorelated/BioD: correct url for undead correct url for undead update the instruction on how to run the example files	5 years ago
George Githinji	b069b71663	update the instructions for running the example code using stream.d from undead	5 years ago
George Githinji	350e6d892a	correct url for undead	5 years ago
George Githinji	91cbb7a49e	correct url for undead	5 years ago
George Githinji	72d5b60fc1	update the instruction on how to run the example files	5 years ago
George Githinji	7441972a6c	merge	5 years ago
George Githinji	5a97817184	bio.bam.cigar module import	5 years ago
George Githinji	7d93484c4f	add bio.bam.cigar module import	5 years ago
George Githinji	a6032f02e2	provide instructions on how to run the example	5 years ago
Pjotr Prins	d0c58c43c5	Merge pull request #1 from biod/master Fixes and refactoring	5 years ago
Pjotr Prins	20274c9fe8	JSON header output fixes #331	5 years ago
Pjotr Prins	f3acb30e16	JSON header output fixes #331	5 years ago
George Githinji	8dde0c5c54	update local repository	5 years ago
Pjotr Prins	bfeef2bfa8	Getting rid of unittest noise	5 years ago
Pjotr Prins	576c0793bf	All unittest output on stderr	5 years ago
Pjotr Prins	21a79f76f9	Roundbuffer: add a few checks	5 years ago
George Githinji	36872d46a1	update from upstream	5 years ago
Pjotr Prins	c6d791fd70	Add URL for zlib	5 years ago
Pjotr Prins	ce54116822	cigar: added nothrow and nogc	5 years ago
Pjotr Prins	7994406592	Moved Cigar functionality into its own module. Reran ragel.	5 years ago
Pjotr Prins	084b867572	Merge pull request #32 from biorelated/master Add fastq support	5 years ago
Pjotr Prins	ba381ee816	Add dub version badge	5 years ago
Pjotr Prins	e9badf0ecb	README: update	5 years ago
George Githinji	a230f2077d	Merge branch 'master' of https://github.com/biod/BioD * 'master' of https://github.com/biod/BioD: fixed #31 (affects reading long SAM records)	5 years ago
Artem Tarasov	c778e4f2d8	fixed #31 (affects reading long SAM records)	5 years ago
George Githinji	8ee68fd34c	Merge remote-tracking branch 'upstream/master' * upstream/master: Update outputstream.d bio/sff/read.d: ulong fix by Matthias Klumpp <mak@debian.org> see https://github.com/biod/BioD/issues/27	5 years ago
Artem Tarasov	aa1152b480	Merge pull request #30 from godotgildor/master fixed a bug in BgzfOutputStream.flush() so that multiple flush calls are supported	5 years ago
Brett T. Hannigan	ba8169dbb8	Update outputstream.d flush() function was not emptying round robin buffer and consequently multiple flush commands could cause the same buffer to be output multiple times. Changed to popFront as we consume each task.	5 years ago
George Githinji	d4358d6671	fix merge issue	5 years ago
Artem Tarasov	61c76b954d	Merge pull request #28 from pjotrp/master bio/sff/read.d: ulong fix by Matthias Klumpp <mak@debian.org>	5 years ago
George Githinji	fba806e897	added a fastq parser	5 years ago
George Githinji	b129008c12	minor formatting	5 years ago
George Githinji	a06f4c21d9	added a fastq parser	5 years ago
Pjotr Prins	bd469c1fdf	bio/sff/read.d: ulong fix by Matthias Klumpp <mak@debian.org> see https://github.com/biod/BioD/issues/27	5 years ago
Artem Tarasov	d7c68e0e11	correct pseudo-bin calculation (thanks @jfarek) lomereiter/sambamba#210	5 years ago
Artem Tarasov	74992c5420	Merge pull request #26 from ximion/master Add Meson build definition for BioD	6 years ago
Matthias Klumpp	815047a6f2	Add Meson build definition	6 years ago
Artem Tarasov	da892d9e31	Merge pull request #25 from pjotrp/master Add compareCoordinatesAndStrand to fix sorting test in depth	6 years ago