github.com/BioJulia/Bio.jl commits | Ecosyste.ms: OpenCollective

WIP writing BigBed files.

71bf51ffe4cb34cc22cf8859acfe3c06d6efea7f authored about 9 years ago by Daniel Jones <[email protected]>

Build and writing BigBed r-tree index.

9f1b8688d5dd7851ae61bc98e6457a459aec0bcc authored about 9 years ago by Daniel Jones <[email protected]>

BigWig write support.

90a49ad0e6090b554d714bf6accdb0e396fb4509 authored about 9 years ago by Daniel Jones <[email protected]>

Work on generating BigBed summarization/zoom data.

b2b5b859a4bbdebe8724e91310475fe1b828b84b authored about 9 years ago by Daniel Jones <[email protected]>

Fix a couple BED read/write bugs.

1bfc3ba8b260a0d6bb41328b46842dd3e4fc6fef authored about 9 years ago by Daniel Jones <[email protected]>

BigBed: Writing headers. Various fixes.

2e6e53c89ab5e6470e586641de8b200ad7c6a23e authored about 9 years ago by Daniel Jones <[email protected]>

Julia 0.4 compat.

e296a4e0a06e4e49d7762a16bdcd8c93050b725e authored about 9 years ago by Daniel Jones <[email protected]>

Fix a couple BigBed output bugs.

31c4fab289bdde4492ff78b1f00bc18ddbff4faf authored about 9 years ago by Daniel Jones <[email protected]>

Iteration over all entries in a BigBed file.

2a16921500e174dbbbafe4521cf32e2a0ddc528e authored about 9 years ago by Daniel Jones <[email protected]>

Fix some type instabilities.

6b7187961521e102f7eea706622724d8027d99eb authored about 9 years ago by Daniel Jones <[email protected]>

Update mmap and docstring syntax.

7c898acf77a66c41d05de9704ac897389071ee85 authored about 9 years ago by Daniel Jones <[email protected]>

Working BigBed searching and reading.

58992ae0c4754fdac7f34fd2577ed8c547041256 authored about 9 years ago by Daniel Jones <[email protected]>

Initial work on reading/searching bigbed files.

4775527e81ff08f6620fde9e1ac0b355fe3cc0ba authored about 9 years ago by Daniel Jones <[email protected]>

Refactor Ragel. Split out reading code into BufferedReader.

bd68454b94d6a739c427ee12481fe50c3e46c20f authored about 9 years ago by Daniel Jones <[email protected]>

Add KmerCounts, analogous to NucleotideCounts.

cfde0aa9dadf1bd7775b0eb99a852b2fb04ab169 authored about 9 years ago by Daniel Jones <[email protected]>

Optimizations to eachkmer.

b20c3cb5df30e0294ea7ab7391279706dc824ed5 authored about 9 years ago by Daniel Jones <[email protected]>

Merge pull request #76 from BioJulia/Ward9250-update-readme

Added waffle.io badges to the Bio.jl README.md

0d8e8cf880034cf3f11254bd7e2993012466e4e3 authored about 9 years ago by Ben J. Ward <[email protected]>

Merge pull request #78 from NPalopoli/patch-1

Minor typo correction

1cafc05577421cb704997f8a48f5b9e3c6d84ea5 authored about 9 years ago by Daniel C. Jones <[email protected]>

Minor typo correction

48e7a2f15e0dff14dc7c10230efb7fd19e07d6bc authored about 9 years ago by Nicolas Palopoli <[email protected]>

Added waffle.io badges to the Bio.jl README.md

a2b68b8f958ebe3e8777a33497cfc3a5914ac978 authored about 9 years ago by Ben J. Ward <[email protected]>

Better EOF halding in ragel parsers. Fixes #75.

a2e7e041f4519026c730c62faf925b8972dc4c15 authored about 9 years ago by Daniel Jones <[email protected]>

Merge pull request #57 from kdmurray91/feat/fqout

Writing of FASTQ sequences

e020e9e7249a8d6dfbcc7d16dbcddc38d8c13c3e authored about 9 years ago by Daniel C. Jones <[email protected]>

Fix all doc syntax occurances

c8641592f84c9d655e0d506d4149860a4ead2246 authored about 9 years ago by Kevin Murray <[email protected]>

Allow 'B' in Illumina 1.5 quality scores

8d160daded64c0bb4d7a5caa3ec1c4ef57c86d39 authored about 9 years ago by Kevin Murray <[email protected]>

Fix FactCheck =>/-->

3fe723245997691e1464376e50e5bc70d998e3c4 authored about 9 years ago by Kevin Murray <[email protected]>

Add encode_quality_string, default stop/start

This adds two functions for encoding quality score vectors as
PHRED-encoded strings (in-place an...

691611bd79d694b07d51467e5ff7792a72dcf1d6 authored about 9 years ago by Kevin Murray <[email protected]>

Copy write(IO, FASTQSeqRecord) back to fastq.jl

Now with added documentation :)

808ccee4d7d78458177b1ea4da571dd93f42b2a2 authored about 9 years ago by Kevin Murray <[email protected]>

Add tests of quality score en/decoding

27538cb4d5dee551f4e778716dadb36edb0cd93c authored about 9 years ago by Kevin Murray <[email protected]>

Fix possible issue w/ illumina1.5 phred scores

7a2239e750f56c61d2f5ab10ae6e00574415e9a5 authored about 9 years ago by Kevin Murray <[email protected]>

Move write(IO, FASTQSeqRecord) to ragel source

5da8196dc7103c34decc95e3455a5b3c3a221dad authored about 9 years ago by Kevin Murray <[email protected]>

Add initial hacky write(IO, FASTQSeqRecord)

fc4dddc7c3c0ad450cdc75aecdeee23030c5e50c authored about 9 years ago by Kevin Murray <[email protected]>

Add missing intervals/Makefile. Strip trailing whitespace from ragel output.

d531283abaa4ad8ebc8c71bf63f2f84e359d41cb authored about 9 years ago by Daniel Jones <[email protected]>

Merge pull request #72 from BioJulia/remove-newlines

Remove newlines

01f0ac70511ee2ee608ee91e0974452f838b396a authored about 9 years ago by Daniel C. Jones <[email protected]>

Merge pull request #73 from BioJulia/safe-precomp

define hash function for Alphabet to compile safely

6232a96e73c717d0a36dc234f48b66b2b8fed199 authored about 9 years ago by Daniel C. Jones <[email protected]>

define hash function for Alphabet to compile safely

12733e0ada82b165db9d38f025fc5b355071b778 authored about 9 years ago by Kenta Sato <[email protected]>

implement equality of AminoAcidSequence

2a5f586492517e96adead198097b116d087a0893 authored about 9 years ago by Kenta Sato <[email protected]>

remove newlines in dna/rna literal

706f703c2787fb311586f5ce222c911054650e94 authored about 9 years ago by Kenta Sato <[email protected]>

Merge pull request #70 from BioJulia/prcastro-patch-1

As promised - it's Saturday and there have been no objections. Remove 0.3 from travis

827f3ea2b98e0778a53a450ab8065c41b4aa65d9 authored about 9 years ago by Ben J. Ward <[email protected]>

Update CONTRIBUTING.md

d62e9779cb4d33e3172c1f0e0a02008e06f39ad9 authored about 9 years ago by Ben J. Ward <[email protected]>

Update CONTRIBUTING.md

db74d95d7f37aae6996486a7de379ff3247f95e1 authored about 9 years ago by Ben J. Ward <[email protected]>

Update CONTRIBUTING.md

8823fab1c6e37f32c91084ec74a81ccdac22b653 authored about 9 years ago by Ben J. Ward <[email protected]>

Merge pull request #69 from prcastro/master

New FactCheck syntax (=> / -->)

08f666366a8d3a575c77231a1b708401fcfec511 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Remove 0.3 from travis

c1ae737bf7a40fda580bcfdd67713f48639b7b67 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Merge pull request #68 from BioJulia/import-ops

import operators from Base explicitly

0bd1bb3a37e3b747d8e160f3225c0feac2988ab3 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

New FactCheck syntax (=> / -->)

fa64378d29ad57e40589b3628ac86c7ee9494985 authored about 9 years ago by prcastro <[email protected]>

import operators from Base explicitly

3560e10b3d27e811560419667fc5afbce1efc1bc authored about 9 years ago by Kenta Sato <[email protected]>

Update syntax in test code.

b58280f9d332fdf76f8ce3acb2abf76fc932338d authored about 9 years ago by Daniel Jones <[email protected]>

Improve intersect(::IntervalCollection, ::IntervalCollection) type stability and performance.

b9f79549851478455340632844416b3d3fc9724a authored about 9 years ago by Daniel Jones <[email protected]>

Merge pull request #66 from BioJulia/opt-getnuc

speed up the getindex method with inlining

0c282a35f9bddc12023a564c32b64a1c88038ef0 authored about 9 years ago by Daniel C. Jones <[email protected]>

Merge pull request #67 from BioJulia/prcastro-patch-1

Typo fix by prcastro

3d9d75bd60ce909b1476161a2ccaff38b5e91e7b authored about 9 years ago by Ben J. Ward <[email protected]>

Typo

Fix type leading to a travis failure

5b4c97ea00b29f3b5ff3119812bc625dedb2e46b authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

speed up the getindex method with inlining

77c93e75d1a4afa4af0a982141d3e78d3b3671df authored about 9 years ago by Kenta Sato <[email protected]>

Merge pull request #56 from dcjones/miscfix

WIP: Optimization/Bugfix Omnibus

c630a52eb0c5d3cfe121bf9dd66d618b2ae79d22 authored about 9 years ago by Daniel C. Jones <[email protected]>

Remove a couple old fashioned docstrings.

a337e2a71550913dfaf7d41cd3f68143bb74fd4d authored about 9 years ago by Daniel Jones <[email protected]>

Fix a couple broken tests.

8f9ec0c512a5021a29034e4f067a3d13e8709844 authored about 9 years ago by Daniel Jones <[email protected]>

Implement IntervalCollection versus IntervalStream intersection.

936b2fcbe5b7c80bd1714deda9994e479c240c0d authored about 9 years ago by Daniel Jones <[email protected]>

Optimization to IntervalCollection iteration.

850bc8410506cb588836504b10dc66393c1f82fa authored about 9 years ago by Daniel Jones <[email protected]>

IntervalCollection bulk insertion constructors.

61cd409e04b354d51f6ef12106f2e5800daa8e22 authored about 9 years ago by Daniel Jones <[email protected]>

Relax sorted requirement for coverage.

3a204d669251a3043523d9a0096bf54deffbacf3 authored about 9 years ago by Daniel Jones <[email protected]>

Fix BED parser not clearing fields between lines.

6d10edb82994e99016cd461fbbd9a63237b6fb93 authored about 9 years ago by Daniel Jones <[email protected]>

Add constructor for NucleotideSequence from Nucleotide vectors.

fd4f5b3cbef857d09dc6d0839ef6a851bcbf6e0b authored about 9 years ago by Daniel Jones <[email protected]>

Add KmerCounts, analogous to NucleotideCounts.

81e7c7a40af2ae0e6a513026a54912302658a8ed authored about 9 years ago by Daniel Jones <[email protected]>

Let parsers read from shell commands.

956bf6be19920054ac86ca796495cdfd84e1dc39 authored about 9 years ago by Daniel Jones <[email protected]>

Add an option to allow ambiguous codons in translate.

Ambiguous codons will be translated to X.

72aefebcd30625bee1a0f137536ae3ac80fdae70 authored about 9 years ago by Daniel Jones <[email protected]>

Add iterator over k-mer de bruijn graph neighbors.

72deb46f0a7181f14b69ca3b5f170fd835ad07da authored about 9 years ago by Daniel Jones <[email protected]>

Fix potential buffer overflow in parsers.

f39323547684daba81b7550c70b3329e4941e9be authored about 9 years ago by Daniel Jones <[email protected]>

Even faster eachkmer.

2e50b530e1bd9c7dfa2c8f52c0f0980686e21a71 authored about 9 years ago by Daniel Jones <[email protected]>

Optimizations to eachkmer.

9d2d8608eba8b3ecf2702f5119e9ad5a41f9c318 authored about 9 years ago by Daniel Jones <[email protected]>

Even faster sequence iteration.

20183971c8451faf60b66af3571d12ea194682ce authored about 9 years ago by Daniel Jones <[email protected]>

Slightly faster sequence reverse.

586f3a3d2c8123a986f7db3cbae423287d21d5b0 authored about 9 years ago by Daniel Jones <[email protected]>

Faster iteration over nucleotides.

7beb054a43458ddd42fe18c0137891996c31c946 authored about 9 years ago by Daniel Jones <[email protected]>

fix AminoAcidSeqRecord

4178e46fdaa242db4c2c69b669f2354d51ad12e6 authored about 9 years ago by Diego Javier Zea <[email protected]>

Merge pull request #61 from prcastro/new_doc_syntax

New doc syntax

196df9fee5c01885a55af2c429ff7fba05fa13d5 authored over 9 years ago by Daniel C. Jones <[email protected]>

Reqire Julia v0.4

8a80e683b35a4d774e283309e89f990d675ae8a5 authored over 9 years ago by brk00 <[email protected]>

New documentation syntax

4b8f6331f1a0967c7b3efc65a3c01efe902eeb51 authored over 9 years ago by Paulo R. O. Castro <[email protected]>

Updated CONTRIBUTING.md - include Julia v number.

da7e4237b9329567e864f861309d32d544c34957 authored over 9 years ago by Ben J. Ward <[email protected]>

Merge pull request #58 from BioJulia/Ward9250-contributing-edit

Updated CONTRIBUTING.md - include Julia v number.

2ae3aab1f383a36579edc12820e9fe0984783264 authored over 9 years ago by Ben J. Ward <[email protected]>

Updated CONTRIBUTING.md - include Julia v number.

652181b1388e06dec0c9e9e52d23d2a84af8b400 authored over 9 years ago by Ben J. Ward <[email protected]>

Merge pull request #53 from dcjones/coverage

[RFC] Interval Coverage

032d367bb8cd014fabf68d1ce706537f0df8dce1 authored over 9 years ago by Daniel C. Jones <[email protected]>

Function to compute coverage over IntervalStreams

52801b6b7d51fe7947b20167345aa2d4908ef422 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #50 from dcjones/intervals-io

WIP: BED Parser

49c6c04671512a4d00f4068453b4aaaf3e189536 authored over 9 years ago by Daniel C. Jones <[email protected]>

Update IntervalTrees diagram to reflect current design.

3e629f8b8dd8f024e78a5d7ee28f0eea3211bf91 authored over 9 years ago by Daniel Jones <[email protected]>

Missing imports.

43691af4ee2635eb9150494ccb542429482a0024 authored over 9 years ago by Daniel Jones <[email protected]>

Fix off-by-one on BED coordinates.

7aa0055bbd82653567e97bf97dbc7990cc007242 authored over 9 years ago by Daniel Jones <[email protected]>

More performance improvements to bed parsing and intersecting.

11294459735921aeee020ddf2c96c0ca09c29904 authored over 9 years ago by Daniel Jones <[email protected]>

Some performance improvements.

75039eabef68341c3578743fdb4beaafb73d46ff authored over 9 years ago by Daniel Jones <[email protected]>

Tests for IntervalStream intersection.

a0876d04f1cb6234d5a5f4a50397df149ef1a029 authored over 9 years ago by Daniel Jones <[email protected]>

Allow '.' and '?' in BED strand field. Print STRAND_NA as '?'.

1053743ab72f615e4d2b1e01fcc0d8ac7f253e9e authored over 9 years ago by Daniel Jones <[email protected]>

BED parser.

6575c136e7b4cb7fb13edf69b1daf11677d10c98 authored over 9 years ago by Daniel Jones <[email protected]>

Add tests for BED parser. Fix a couple bugs.

819e7e79ad2760b11cb8f257af29f94890b7124e authored over 9 years ago by Daniel Jones <[email protected]>

Fix a parsing integers.

a99d9539d5eb1ab309ef40dfe0567b569ef148c7 authored over 9 years ago by Daniel Jones <[email protected]>

Fix test command

6d4d4d37962c6ba2fd71230821a02a6033fc4a88 authored over 9 years ago by Richard Smith-Unna <[email protected]>

Moar typos

df3156546c3e801c6de704f5c5de87bb2e707582 authored over 9 years ago by Richard Smith-Unna <[email protected]>

Merge pull request #32 from dcjones/intervals

Intervals

f9842867514851524878f232d86b54a6d76288a9 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Fix style inconsistencies and uneeded type parameters.

8c0e96195918931cb2dfaaef90254c9497b07516 authored over 9 years ago by Daniel Jones <[email protected]>

Document a couple things. Explicitly import Base methods.

cc33622f4eca8b6f3aa7f2afcfa550bb7f6f706d authored over 9 years ago by Daniel Jones <[email protected]>

Rearrange and add tests.

3f70d7d700d6a0e25fb70216f0f60c86eae260d3 authored over 9 years ago by Daniel Jones <[email protected]>

More tests.

de4e7c5ad4a92a145013925605508b6f8467dfe0 authored over 9 years ago by Daniel Jones <[email protected]>

Add Distributions to test/REQUIRE.

3cc5f7d65e3c5540adaa5e619b1ab642cf4dea13 authored over 9 years ago by Daniel Jones <[email protected]>

Split intervals.jl into several files. Organize tests.

79fe55212077b4b7ba37d302e308dfda2aa94871 authored over 9 years ago by Daniel Jones <[email protected]>