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

Merge pull request #112 from BioJulia/fix-anchor

fix printing of anchor

266691f7b0696938f6349cad12283b93e17b2c8d authored about 9 years ago by Daniel C. Jones <[email protected]>

fix printing of anchor

efa76502c719003ca6c9010dc0364527fbe047f8 authored about 9 years ago by Kenta Sato <[email protected]>

Merge pull request #110 from BioJulia/align2

Align Redux

16c9b49295dd4814d4fd0de900d06a77b2a50cd3 authored about 9 years ago by Daniel C. Jones <[email protected]>

Minor improvements.

6ac33f91edc2f15557187434c719cba22607b002 authored about 9 years ago by Daniel Jones <[email protected]>

Add a little documentation.

7d9a6c617c675ed678b317900ef7f30540aea109 authored about 9 years ago by Daniel Jones <[email protected]>

Fix accidentally disabled tests.

0214bd7f50259a06440734f0c16f77b423085883 authored over 9 years ago by Daniel Jones <[email protected]>

Temporarily remove alignment position mapping.

f43b9c2ea1adbf743e2b73d92fc1c1835a310281 authored over 9 years ago by Daniel Jones <[email protected]>

Cigar string conversion.

aff32df910ee564e7ce972bbe9bdb3945536d376 authored over 9 years ago by Daniel Jones <[email protected]>

Some reworking and testing of anchor encoded alignments.

99cd68066163e427c97380ea5f8207543ce3438d authored over 9 years ago by Daniel Jones <[email protected]>

Remove gaps and cigar for now.

71d529dfa99342215d4ece7420a5ee70606d0948 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #108 from BioJulia/import-hash

import hash from Base

0697dc92bc8394d447a6ec3e99454f3d59b2d471 authored over 9 years ago by Kenta Sato (佐藤建太) <[email protected]>

import hash from Base

4fd8964ecbe737f674161246333f7d3a7208e490 authored over 9 years ago by Kenta Sato <[email protected]>

Merge pull request #106 from BioJulia/ragel7

Regenerate parsers with ragel 7.

571c954ec4112960c1feeed0a1c9ad11116c5185 authored over 9 years ago by Kenta Sato (佐藤建太) <[email protected]>

Regen parsers using const globals.

1838751912ea63248685ca1aef49f728641c64ba authored over 9 years ago by Daniel Jones <[email protected]>

Encode CIGAR as it is in BAM.

961538d8bbe0aae8eae091612e07250703acb01b authored over 9 years ago by Daniel Jones <[email protected]>

Fix style.

* Don't use camel case.
* Julia 0.4 deprecations.
* No longer need `@doc ... ->`

a7089ab0233fb21f138e5d3ae156da62c847e3a3 authored over 9 years ago by Daniel Jones <[email protected]>

Initial draft of alignment representations.

e4042fa36af26468ba80bd3f86b2ea06885356da authored over 9 years ago by Ward9250 <[email protected]>

Regenerate parsers with ragel 7.

e4b14d5922811e4313412ddc5ff4687002cbedb7 authored over 9 years ago by Daniel Jones <[email protected]>

Nothing -> Void

9545c3f7d3100dcc260f3d772373c246b1ff410e authored over 9 years ago by Daniel Jones <[email protected]>

Fix a couple deprecations.

2224a458fa54b0964c7a039a7dae7a6f67615036 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #93 from BioJulia/conv

add `convert` to a byte sequence from bio sequences

a17fa523591a9d1e419d0e1fae8c05567a68b0fe authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

use cld

ecb7fcc14da60bc19bef79d3dc46869c1baa3952 authored over 9 years ago by Kenta Sato <[email protected]>

use `falses` to make bitarrays

cf94553abf689288704df98e78d7b18efee3aa8b authored over 9 years ago by Kenta Sato <[email protected]>

a few touch-ups of document strings

2e42203646f04cd07a23b92a1716a04995c38775 authored over 9 years ago by Kenta Sato <[email protected]>

fix style of `Union`

833c6fa1503fcfab98cc0476e98647f97664e462 authored over 9 years ago by Kenta Sato <[email protected]>

use more conversions

aad919f660f26ff871e05e4cffb73a80e8332fa7 authored over 9 years ago by Kenta Sato <[email protected]>

Merge pull request #100 from BioJulia/round-trip

Round trip tests for reading/writing. And some bug fixes.

1114a9aa8205be91a846fa733e60e60546379b30 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Round trip tests for fastq.

0df77a16e5dcf72b1298468d69ccb4a0f299a498 authored over 9 years ago by Daniel Jones <[email protected]>

Round trip test for BED.

88f95026b141bca2c534921663b1d5119a3aa786 authored over 9 years ago by Daniel Jones <[email protected]>

Add round-trip tests for fasta. Fix a bug in AminoAcidSequence.

b65fcbe24eccf9aabf641f891d4dd7079ab8cf36 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #99 from BioJulia/prcastro-test-show-rna

Test show method for RNA nucleotides

bd48fc9f1ce25354d35a861466e74a56f05a5555 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Test show method for RNA nucleotides

969ddd57b33ba60ab96bea9994bf3886d3405177 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Broaden FASTA write definition.

2a2d8413d58518a5dc0cf9df1093a9a6a50bb983 authored over 9 years ago by Daniel Jones <[email protected]>

delegate conversion of nucleotides by calling function show()

8160b82daf7e0b6f476ddece31b2abd679fb0c3a authored over 9 years ago by wildgarden <[email protected]>

enhanced test: 2 sequences with description

8e39eea890c0d4f1d607cb005aa5acb57dfc8bc6 authored over 9 years ago by wildgarden <[email protected]>

added Base.write() to support writing of FASTASeqRecords to IO-Streams

6081c32c52479f1f54e87da631c85e2eb6312e53 authored over 9 years ago by wildgarden <[email protected]>

Add a link to the manual.

d0c8881f1edebf8ff6a9d44e3d3884343b2d6dca authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #92 from BioJulia/docs

Generating a manual

df19f272ac826bfed9db0ca99fa03e1e1d9ee17c authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Merge pull request #98 from BioJulia/show-nucs

import the write method into Bio.Seq from Base

057041de79f91171ac9e97bc1abb8231a904f6ca authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

import the write method into Bio.Seq from Base

9927727a1d55b021228c5f12ce5ef667aa063db6 authored over 9 years ago by Kenta Sato <[email protected]>

Fix a docstring.

004c6c08827efe93b75313684df433e20781fde2 authored over 9 years ago by Daniel Jones <[email protected]>

More parsing docs.

f227966a95c290ffebc03938abcc2ff9e9319f2e authored over 9 years ago by Daniel Jones <[email protected]>

Work on documentation for Seq module.

b1c6a3537aa697667590224c7f1cbecf9053b578 authored over 9 years ago by Daniel Jones <[email protected]>

Put a something in index.

f0a3add48e9459a023d5f1542b14d6bce64fe819 authored over 9 years ago by Daniel Jones <[email protected]>

Some documentation for Intervals.

1330d3d38519baaa8d66ad2839ca1a7b40a22ef3 authored over 9 years ago by Daniel Jones <[email protected]>

Some more parser documentation.

c60bafaad7dd4f565c09b4d9c7e64eb4f452ad82 authored over 9 years ago by Daniel Jones <[email protected]>

Start documenting parsing.

2f017da4dac06d63acd904b18276010946d93f4b authored over 9 years ago by Daniel Jones <[email protected]>

Add some simple judo-style docs.

7dafdd1d80920133c43290dfefeb5f922d6aa25c authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #97 from prcastro/code_refactor

Code refactor

5ee324be74a67d1eb4bd071ac9156016650682b5 authored over 9 years ago by Kenta Sato (佐藤建太) <[email protected]>

Rename module files

02849132eeaee80fa328bc2299e8f98994c91628 authored over 9 years ago by prcastro <[email protected]>

Minor bug

4f308f387f7bb3386c5235f7acd9f3c7b4adf5a4 authored over 9 years ago by prcastro <[email protected]>

String -> AbstractString

3dfd144584fa5edeb0cf97f1e881a1a14e734e81 authored over 9 years ago by prcastro <[email protected]>

Remove Compat, Docile, change Uint -> UInt and split using/import/export statements into lines

18d1f4ab521b3907a8f57338c61ee96b1cf63297 authored over 9 years ago by prcastro <[email protected]>

Merge pull request #85 from dcjones/io2

Parsing Infrastructure Iteration

48c025980eb88007db0c19f5ea688c864903d1f5 authored over 9 years ago by Daniel C. Jones <[email protected]>

Remove some Base. qualifications.

fe28ba3686cb61fcecb77c225f7fa8c6f9ee892a authored over 9 years ago by Daniel Jones <[email protected]>

Move StringField to a module. Get rid of ParseImpl modules. Import things.

a14b2a10b9d4031ce4ab00e6957199f8c81408d0 authored over 9 years ago by Daniel Jones <[email protected]>

Fix parsing AminoAcidSequences from FASTA.

71ccd8cb25b151d2610c8f4c6324e1bfda8aadb2 authored over 9 years ago by Daniel Jones <[email protected]>

Zlib -> Libz

962e567b6cc834ee32ee77b97d6037fd0efe2a75 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Update BigBed parser and writer.

608638d5d7fefb13b209bab61d524eaf6edd8d62 authored over 9 years ago by Daniel Jones <[email protected]>

Update BED parser.

9d22f8597ecb60ac62260dd83b267f1aae88b688 authored over 9 years ago by Daniel Jones <[email protected]>

Update FASTA parser to new system.

6f82111295ff0a496d4b2019da8ab0ffac0d5ace authored over 9 years ago by Daniel Jones <[email protected]>

In-place fastq parsing. Faster NucleotideSequence encoding.

b57e3aac5ddff63091b713771b238640f70cbe0f authored over 9 years ago by Daniel Jones <[email protected]>

Fix regression in IntervalCollection versus IntervalStream intersection.

733a06249361285d9e641e615543bbc8e5b1abfa authored over 9 years ago by Daniel Jones <[email protected]>

Fix some FASTA bugs.

62aff433ddbd7db43db5139707be9fbb85171030 authored over 9 years ago by Daniel Jones <[email protected]>

Automatic iterators. Better quality encoding inference.

a6b08e4eaa99d637a1db3850a4199463747ca739 authored over 9 years ago by Daniel Jones <[email protected]>

Make intervals mutable.

94097699441e80642de7934fe1a7085ffc5c0874 authored over 9 years ago by Daniel Jones <[email protected]>

Mutability for AminoAcidSequence.

ae7b05ac7532d5ba7d01c2ce5ed923f57e19108e authored over 9 years ago by Daniel Jones <[email protected]>

More work on parting to BufferedStreams.

fd22553b98243c7c2f2c0bd1cac295ac25e0a4ca authored over 9 years ago by Daniel Jones <[email protected]>

Some optimizations.

16babdd5714d1b0fac26d576a1ef60733ec1558d authored over 9 years ago by Daniel Jones <[email protected]>

Start moving parsing over to BufferedStreams.

55812479e64771d7af12d6349c01e9a28bfffec8 authored over 9 years ago by Daniel Jones <[email protected]>

Use nightly instead of 0.5 in travis.

2ba7d2795dfec0dcde2b338d9915992d16361c20 authored over 9 years ago by Daniel Jones <[email protected]>

Update travis to run on julia 0.4 and 0.5.

7eca8f050428e15adfb4fa353b3b23066846813b authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #94 from dcjones/codecov

Add Codecov support.

f9105fcd61ff0c4c0f20f8568ca58f4cf391297f authored over 9 years ago by Daniel C. Jones <[email protected]>

Merge pull request #37 from dcjones/mutable_seq

Mutable Sequences

d6e07c1a3c78ae616e013246c4abe55cff55b070 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Add some tests. Fix orhpan! functions.

4b9671d0c81e83b1bb5523a2bf873982e4f8c780 authored over 9 years ago by Daniel Jones <[email protected]>

Use reorphan parameter on orphan!(::AminoAcidSequence).

2d2b277c6934578c3cb343539c3e82ea55414dbc authored over 9 years ago by Daniel Jones <[email protected]>

Address some review comments.

66bd56857e876fbadbcd8a5752c5e0374a3ddbcd authored over 9 years ago by Daniel Jones <[email protected]>

Mutability for AminoAcidSequence.

8087d9026352d2101c7f1376d9f8dd0619fdda73 authored over 9 years ago by Daniel Jones <[email protected]>

Basic tests for mutable sequences.

3f099f9e2d9cdd613e6ebd2661f92824d0023c2a authored over 9 years ago by Daniel Jones <[email protected]>

Basic mutable nucleotide sequences.

16654a8b336f72615bf3fd9fcfe27e3cab4a43e4 authored over 9 years ago by Daniel Jones <[email protected]>

Add Codecov support.

59b87c1b7aaceffa51792b7959271f589347894d authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #89 from BioJulia/Blahah-patch-1

Add getter/setter policy (see #25)

de004dd0789c75596c1cd4b7bd1ab0d4d6abebf9 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Merge pull request #88 from Ward9250/editorconfig

Added editorconfig file

ebea5d340ed23eaebc4b3595047c7c3d6b41b709 authored over 9 years ago by Richard Smith-Unna <[email protected]>

Add getter/setter policy (see #25)

f93eb9ade6808fa89a3f76ff2b1fe697ffff0511 authored over 9 years ago by Richard Smith-Unna <[email protected]>

Altered pattern to include julia-hosted ragel files

e833dacc8aabfdf0584f838743ed4f30e1089047 authored over 9 years ago by Ward9250 <[email protected]>

Added editorconfig file

134775a466a88afede82098310572ee3ed7ed53e authored over 9 years ago by Ward9250 <[email protected]>

Change next method for aminoacid

37427035d68fa3e98b437ca050485603b857ccd8 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>

Merge pull request #51 from dcjones/bigbed

BigBed/BigWig reading and writing

7e1e9ec90149e9b2524ae5abd080c4f5b94a90d6 authored over 9 years ago by Daniel C. Jones <[email protected]>

Add Zlib to REQUIRE.

a283eea994afc19f86a8075d44930676b24af9bc authored over 9 years ago by Daniel Jones <[email protected]>

Remove more junk from merging.

71c9c00dddff6e48fa396eaf007d68a72e51a9e6 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #83 from BioJulia/fix-subseq

Fix subseq

f6e89dcf201658b826493527e713cc765c9f3453 authored over 9 years ago by Daniel C. Jones <[email protected]>

add tests for subsequence of subsequence

6401a54d6f42ad888a505850cc40d1a87cec026f authored over 9 years ago by Kenta Sato <[email protected]>

fix #82

cb595c6c8baf4b7acd1ee4024ff3fc0f281bc432 authored over 9 years ago by Kenta Sato <[email protected]>

Merge pull request #81 from Ward9250/update-travis

Update travis

bb189ce139b06719812f22003f08ce04589c9e1b authored over 9 years ago by Daniel C. Jones <[email protected]>

Trying the setting in travis.yml for the new container architecture they say is better

e1392cdc51082df3a426d4485e168fc52f26b950 authored over 9 years ago by Ward9250 <[email protected]>

Remove some left over merge junk.

e88ea5eb5b0b461a06695601840ee66cfe22a8c7 authored over 9 years ago by Daniel Jones <[email protected]>

Fix fillbuffer! logic.

34ed8988961a11477ef0fbe2af4f6485f05d5fd1 authored over 9 years ago by Daniel Jones <[email protected]>

Test BigBed intersection. A couple fixes.

354aa7b906c8d487ea57d2855032f07ce8b6d69b authored over 9 years ago by Daniel Jones <[email protected]>

Start adding BigBed tests. Fix some bugs.

0c050e8f8bb3a0690ed726059c6369f4b4a86483 authored over 9 years ago by Daniel Jones <[email protected]>

Fixes for BigBed iteration.

63c2c70c0113a4895247fe1ac7eaa97eec0e9fa2 authored over 9 years ago by Daniel Jones <[email protected]>