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github.com/BioJulia/Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl

Julia 0.4 compatibility

44fffdc612259a505a2594f0cc5aedc05362cf02 authored over 9 years ago by Daniel Jones <[email protected]>
Limit ⋮ usage for showing IntervalCollections

Show the `⋮` for an IntervalCollection only if the number of entries exceeds the number of entri...

83a73004ed98c7ba271b10005361eb7e68ea30a6 authored over 9 years ago by Julian Gehring <[email protected]>
Some tests and fixes.

96f0b8f0aa2f261913a9759fe0089fe45d514292 authored over 9 years ago by Daniel Jones <[email protected]>
Intersection for interval streams.

06eff246a63d9e9c996c52e6046d58eb98033753 authored over 9 years ago by Daniel Jones <[email protected]>
Rewrite IntervalCollection using new IntervalTrees.

70c61a49c8a485e8e1dada5f56755330557f035b authored over 9 years ago by Daniel Jones <[email protected]>
Show empty IntervalCollection

Fixes the `show` method for an empty `IntervalCollection`. Before,
IntervalCollection{Int}...

951df41e15822a9a43bb791051ee7953d0bb4940 authored over 9 years ago by Julian Gehring <[email protected]>
More natural ordering for seqnames in IntervalCollection.

12f9adc4040f7294ba5693b55cf73c1eef30e81b authored over 9 years ago by Daniel Jones <[email protected]>
First pass at intersect for IntervalCollections.

3d2fbbe6c0a6f2cf047d9135d85d25c92dbe6fa6 authored over 9 years ago by Daniel Jones <[email protected]>
Add missing file.

e3654ee22aeaf2423426b0a4f004cf9e27e13ac4 authored over 9 years ago by Daniel Jones <[email protected]>
Rename IntervalSet → IntervalCollection

ab7bfba0c3d3e3c28581092f3079a0480bd600e9 authored over 9 years ago by Daniel Jones <[email protected]>
Initial work on genomic intervals.

ecc3bc4af7685446ccf1e590491a7f6d35e21e68 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #40 from dcjones/io

RFC: Parsing infrastructure, FASTA and FASTQ parsers

618bad333b6bbdefe0af2cf2a6e1c907bb52a773 authored over 9 years ago by Daniel C. Jones <[email protected]>
Fix first letter of descriptions missing in FASTA and FASTQ.

8cce44dae8d61e246a8284a1e795681ab191715b authored over 9 years ago by Daniel Jones <[email protected]>
Julia 0.4 compatibility

f0c206912e427949d885fa3e5287e9b370f8a4a0 authored over 9 years ago by Daniel Jones <[email protected]>
Regenerate parsers with updated ragel: no unecessary begin/end blocks.

eba27c2322500c6e5b25523e8bce1faa3bc2bc28 authored over 9 years ago by Daniel Jones <[email protected]>
Explicitly import some Base methods.

057bf0500c355957c5472794daaf06a13c40e482 authored over 9 years ago by Daniel Jones <[email protected]>
Minor FASTA/FASTQ optimizations.

b6987934dc85c1f0efc97713d06594f903e3c0a0 authored over 9 years ago by Daniel Jones <[email protected]>
Split SeqRecord types out of seq.jl.

12489c19b22137cb502d544743575c5ab2ebf68b authored over 9 years ago by Daniel Jones <[email protected]>
NucleotideSequence optimizations.

0304e9ed14fb034375b7f678a66a311eebba373d authored over 9 years ago by Daniel Jones <[email protected]>
Add warning messages to the top of generated files.

9b46dedc6b130d8989697f203b8b7b5781be7634 authored over 9 years ago by Daniel Jones <[email protected]>
Organize parsing tests.

d1cc1517f482635c2569cd5f798212631e200f3d authored over 9 years ago by Daniel Jones <[email protected]>
Optimizations to FASTQ parsing.

a1a843648e40851ea9933f3d35f7bfc9914a04bb authored over 9 years ago by Daniel Jones <[email protected]>
Fix a bug that can occur when parsing large files.

1ca85ec98d2a5bde4b43b650b6c730852759a203 authored over 9 years ago by Daniel Jones <[email protected]>
Minor simplifications to FASTA and FASTQ parsers.

e91f58bd12eebc5d2c41a7b1adad65b6a9a4db6f authored over 9 years ago by Daniel Jones <[email protected]>
Require Switch. Don't require FactCheck, that's in test/REQUIRE.

8e41f82040be45d410f8d982ed321940ab38306e authored over 9 years ago by Daniel Jones <[email protected]>
Use direct unbuffered file io.

79f0f64a050f90ce38c8df5124efc34c60c0bf8b authored over 9 years ago by Daniel Jones <[email protected]>
Some performance improvements to sequence parsing.

1ada64d040cfaadfdf05f8134d29c76b814b4e98 authored over 9 years ago by Daniel Jones <[email protected]>
Automate fetching of BioFmtSpecimens for tests.

e9a8df1533707716a7f960a8839c153aafc4fd81 authored over 9 years ago by Daniel Jones <[email protected]>
Parsing infrastructure and parsers for FASTA and FASTQ.

40eadd2e0b13359738da70525573a52c2dc5163e authored over 9 years ago by Daniel Jones <[email protected]>
Test parsing memory mapped files.

9513eab13a6d88ca2e7c9e5c7486ac710e7f1549 authored over 9 years ago by Daniel Jones <[email protected]>
Fix tests on Julia 0.4

71a5e1247a080cd713a441abd81753df109ca3f8 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #49 from dcjones/contributing

Add a basic CONTRIBUTING.md

937679bd0f016f30ef1f6e58b62f9a52dc12214b authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #47 from brk00/master

[Seq] More documentation

e638be60cc98efdea1c45a9bf074af1f3313700e authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #2 from Blahah/patch-1

Typo

2a9d866d3d42ddaa3165ef624eee06585c123be7 authored over 9 years ago by Daniel C. Jones <[email protected]>
Typo

75246be7b72915bb71599b949ef72961d62a0441 authored over 9 years ago by Richard Smith-Unna <[email protected]>
Link to julia ommunity standards.

81addc8559a02f1afb5ca1bf6a274ac361eec458 authored over 9 years ago by Daniel Jones <[email protected]>
Spelling, typos.

62a9bfb0cb64110e34cb6965222513e46e91709d authored over 9 years ago by Daniel Jones <[email protected]>
Fix typo.

a06cf7a47e48644c71484003732d393bf696e5b9 authored over 9 years ago by Daniel Jones <[email protected]>
Don't indent module contents.

b462454c1eadf0894f194ddf4f39ad780256aefa authored over 9 years ago by Daniel Jones <[email protected]>
Corrected mismatches docs

a620102e61794e41422c4cce7bd5eca0078031aa authored over 9 years ago by brk00 <[email protected]>
Clean up CONTRIBUTING a little.

d92c360d3b6856fece457d61f91263513f3fb56f authored over 9 years ago by Daniel Jones <[email protected]>
Add a basic CONTRIBUTING.md

f3b4c0fbaf313cd28f06030583982e5f2f5be0e8 authored over 9 years ago by Daniel Jones <[email protected]>
More docs and @assert into EachKmer constructor

0450833e4c579ea89ffedbade7164796fd86bd95 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
More docs

824c00e16ce7a952842ab16d6010510c35f618c6 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Import complement from Base

a088a9816ad85f2ccce0290eb494bdec348eb7e4 authored over 9 years ago by brk00 <[email protected]>
Missing quotes

5f81de7363962fdc0f46709c2cd59aff7318bd00 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Missing arrow

18be68aa92e8f313a98b5e3e32c650549aa5e080 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Undocument bitstype

f3654c3dac95cc80aad28bc9d17afbb4450e1b52 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Seq: more documentation

8443e480f12e995e408979b2cff3c93b90eefa00 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Seq: more documentation

c4c6038d3ee747968716d92dd41c4770e63f99cf authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Explicitly import

7c03ef1a4d84d33d03948f177f23a43bb72ac24c authored over 9 years ago by Daniel Jones <[email protected]>
Simplify some code. Fix spelling.

ec71c316e6d87b6da8877a71d7910f6469803455 authored over 9 years ago by Daniel Jones <[email protected]>
Add concat '*' and repeat '^' operators for sequences.

b180363afa3d12a6995a5756f4c91088fcd9fbbb authored over 9 years ago by Daniel Jones <[email protected]>
Concatenation for sequence types.

7005f4ae54d6e737929d570f3786c25a4e872e15 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #43 from bicycle1885/parse-aa

add parse method for amino acids

59bc8abcb44c76a695536c30ad9eb5376b2e4b5d authored over 9 years ago by Daniel C. Jones <[email protected]>
import parse function from Base

33f63754d16f17da9b9e7e04614f3dda2c3764a7 authored over 9 years ago by Kenta Sato <[email protected]>
remove exception types of tests

2ae1f53ba8e8752b3b8a81eaba355e1eedf335cc authored over 9 years ago by Kenta Sato <[email protected]>
add tests for the amino acid parser

83113a60579cdfa9471e06e986ba3bb8f5f2a06d authored over 9 years ago by Kenta Sato <[email protected]>
add parse method for amino acid

fcf0b1abbde82efa235e4aafb5f6abf361519918 authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #41 from bicycle1885/clipboard

add the 'clipboard' methods for sequence types

ccf244bbd66fe4edb4795158a1b21d802690f728 authored over 9 years ago by Richard Smith-Unna <[email protected]>
add the 'clipboard' methods for sequence types

2f6f633936ec55cd1d01595361bf23540f25d96c authored over 9 years ago by Kenta Sato <[email protected]>
fit sequence printing to the window size

993712a901d7654aa11115d4d9e8d819756084b4 authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #35 from bicycle1885/compl

make unsafe_complement! return a transformed sequence

1bcb6d8655508ee35c1f20b8de9b61544cbcd647 authored over 9 years ago by Daniel C. Jones <[email protected]>
make unsafe_complement! return a transformed sequence

which is a standard behavior of destructive functions
(cf. Base.push!, Base.append!, etc.)

8bbadb5d6d07c859f3c8527fcb6c56f7ecb6561b authored over 9 years ago by Kenta Sato <[email protected]>
Merge pull request #34 from brk00/seq_tests

[Seq] More tests, less bugs

609c0c4fd787b519eada86d7e73d2a67a3b8198f authored over 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #1 from dcjones/seq_tests

Julia 0.4 compatibility.

5ce0e1d2b8ac3ff8a9fbb5945df5d89bd9aa3627 authored over 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Julia 0.4 compatibility.

682706bccdd7ab02dd811b7eae99e697f57d8337 authored over 9 years ago by Daniel Jones <[email protected]>
Even more tests

75d8614e6868c83c35824d7f10ff1c652e50fcbf authored over 9 years ago by brk00 <[email protected]>
More tests for Kmers

4b31ee548d77fb17f757fbf962c51e6023abe7f2 authored over 9 years ago by brk00 <[email protected]>
More tests and export isless

217bb73642faf5667b37571c732ebde8f341dcaf authored over 9 years ago by brk00 <[email protected]>
More tests for Kmer from/to NucleotideSequence conversions

2da5c24e33b065a179df81b448b93a423b06408f authored over 9 years ago by brk00 <[email protected]>
More reorganization of nucleotides tests

7207523f74481ccedaf5429dede9f4e524653556 authored over 9 years ago by brk00 <[email protected]>
Solved bug with nested facts, reorganization of Transformations and Aminoacid Sequences tests, added some more tests

b8f4fdec38d309a3be230d607ab4b996ed55c5de authored over 9 years ago by brk00 <[email protected]>
Simplified kmer conversions

08aa72af1f5403320da12ae5f3f7a118d2150297 authored over 9 years ago by brk00 <[email protected]>
Added more tests and introduced BoundsError() on NucleotideSequence next method

0c87448fe45300903b6677137e925ec4f4830577 authored over 9 years ago by brk00 <[email protected]>
Added tests and solved bug with rnakmer construction from RNASequence

cb91a2caa9a029f028eda49133d0e0e4f8799458 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Modernize travis.yml.

a984e8d077e1ff5a152b62be2707013751ed0fe3 authored over 9 years ago by Daniel Jones <[email protected]>
Merge pull request #33 from brk00/master

Added 26 tests for Nucleotide Sequences

515e77c7a57fd67d0bf1c66ca47360c2cc70f130 authored over 9 years ago by Daniel C. Jones <[email protected]>
Added 26 tests for Nucleotide Sequences

8936fd0bf77f68a7b791a3dfc5dbe7c6110427f4 authored over 9 years ago by Paulo R. O. Castro <[email protected]>
Merge branch 'master' of https://github.com/brk00/Bio.jl into brk00-master

6d4734149424d92cac7417714a38b4fb8d6f64ca authored almost 10 years ago by Daniel Jones <[email protected]>
[Seq] Reduced the number of files

0bdabcc86af992fd6b125467187a76787453374a authored almost 10 years ago by Paulo R. O. Castro <[email protected]>
Fix julia 0.4 deprecation warnings.

bb06cc5995fd224a796ef1951aea0b2364f1e7dd authored almost 10 years ago by Daniel Jones <[email protected]>
Merge branch 'brk00-master'

144290623eee26f9e9cf9bf5dc4bed1b343855c5 authored almost 10 years ago by Daniel Jones <[email protected]>
Merge branch 'master' of https://github.com/brk00/Bio.jl into brk00-master

965d59390de207c42243005570450d8a496a26be authored almost 10 years ago by Daniel Jones <[email protected]>
Merge pull request #30 from julian-gehring/patch-show-nt

Fix show methods for nucleotide input

6910e9bef5d81e7c29574f55aec91d2449811051 authored almost 10 years ago by Daniel C. Jones <[email protected]>
Fix show methods for nucleotide input

Has referred to the non-existing variable 'aa', should refer to the input 'nt'

61ee874371af6df2f46c6d94c501f0e70edc6c89 authored almost 10 years ago by Julian Gehring <[email protected]>
Improved kmer nucleotide counting + tests + fixed tests regressions ('Transforms')

f6ce2125982c59160ff2300f3e6dd1f26d79c177 authored almost 10 years ago by brk00 <[email protected]>
aminoacid => amino acid

2512a82a7077ab95a526e2fc21826efad0b866ff authored almost 10 years ago by brk00 <[email protected]>
Fixed regressions and tests

630c5cbeefc3915d48b2022209f2b4675ff5ec66 authored almost 10 years ago by brk00 <[email protected]>
[Seq] geneticcode.jl bug and formatting

c6e20299abeda86b678a7b7d2052b2fb575ee966 authored about 10 years ago by brk00 <[email protected]>
[Seq] Code refactor and bug solving

825a35bb1211f1d1ab62f260880227cc844969d1 authored about 10 years ago by brk00 <[email protected]>
Equality operations for sequences and kmers. Fixes #21.

a7ecba5d52709d2c8b89e4a6e4e003358b002eab authored over 10 years ago by Daniel Jones <[email protected]>
Faster nucleotide_count with large numbers of Ns.

974015a3f5eaa5f7792bb4a879ff017cd0fc6247 authored over 10 years ago by Daniel Jones <[email protected]>
Enable coveralls. SVG badges.

9d70e78aa417bb3467b4781c4faa1c5eddad1fa2 authored over 10 years ago by Daniel Jones <[email protected]>
Merge branch 'seq'

98cd657ebc6a77300d2fde6ca020cbf3f881d425 authored over 10 years ago by Daniel Jones <[email protected]>
Make printing of sequence types a little nicer.

3236134ba6740d28912b5da428f99a5da0664b38 authored over 10 years ago by Daniel Jones <[email protected]>
Merge pull request #15 from dcjones/seq

WIP: Sequences

29a11dba3afba71483a97880d57ba2d3ea29922a authored over 10 years ago by Daniel Jones <[email protected]>
Kmer tests.

aa1fd9c2afa0189bfd3fc347ca58aafae15b4226 authored over 10 years ago by Daniel Jones <[email protected]>
Handle translatable ambiguity in translate.

c4c8a5250a304055236c178ae96fce0f3b7c9131 authored over 10 years ago by Daniel Jones <[email protected]>
Test . Fix a few things.

c8335d09b71f2844c72ee817bc899af234e2e2c1 authored over 10 years ago by Daniel Jones <[email protected]>