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2bit-encoded reference reader #31

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merged 1 commit into from Mar 7, 2017
Merged

2bit-encoded reference reader #31

merged 1 commit into from Mar 7, 2017

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alumi
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@alumi alumi commented Mar 3, 2017

Added a reader for 2bit reference file format.
Also added test files converted by faToTwoBit

.2bit is a compact randomly-accessible format of DNA sequences.

(with-open [r (cljam.twobit/reader "PATH/TO/2BIT")]
  (cljam.twobit/read-sequence r {:chr "chr1" :start 1 :end 1000}))
=> "ATGC..."

Maybe we should have some protocols or some abstractions for range-based querying (read-sequence) for FASTA and 2bit.

@alumi alumi requested a review from totakke March 6, 2017 04:32
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totakke approved these changes Mar 7, 2017
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LGTM

@totakke totakke merged commit 14d4d9c into master Mar 7, 2017
totakke added a commit that referenced this pull request Mar 7, 2017
@totakke
Merge pull request #31 from chrovis/feature/two-bit-reader
79e7b4c 
2bit-encoded reference reader
@totakke totakke deleted the feature/two-bit-reader branch March 7, 2017 03:01
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totakke commented Mar 7, 2017

Thanks!

Maybe we should have some protocols or some abstractions for range-based querying (read-sequence) for FASTA and 2bit.

I think so, too. SeqReader or RandomSeqReader looks good.

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@alumi @totakke