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BioJulia / Bio.jl / 2213
64%

Build:
DEFAULT BRANCH: master
Ran 30 Aug 2016 07:05AM UTC
Jobs 3
Files 100
Run time 12min
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kdmurray91
BAM and SAM formats (#265)

* add BAM/SAM file formats

* add tests

* add tests on SAM

* add more tests

* clean up

* update some docs

* update docs

* rename variables

* fix SAM

* fixup! fix SAM

* fixup! fixup! fix SAM

* address Ward's comments

* address Murray's comments (and fix typos)

* fixup! address Murray's comments (and fix typos)

* rename refid => refindex

* fix slow copy of SAMRecord (hope to fix the CI failure)

* read a SAM header before parsing

805 of 805 new or added lines in 17 files covered. (100.0%)

5615 of 6912 relevant lines covered (81.24%)

3385245.54 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
100.0
src/align/hts/sam/reader.jl
2
100.0
src/intervals/index/bgzfindex.jl
3
100.0
src/align/hts/bam/bai.jl
3
100.0
src/align/hts/bam/intersect.jl
3
100.0
src/align/hts/sam/header.jl
3
100.0
src/intervals/index/chunk.jl
4
100.0
src/align/hts/sam/sam.jl
5
100.0
src/align/hts/bam/auxdict.jl
5
100.0
src/align/hts/bam/bam.jl
8
100.0
src/align/hts/bam/reader.jl
17
100.0
src/align/hts/sam/record.jl
19
100.0
src/align/hts/bam/record.jl
44
100.0
src/intervals/index/tabix.jl
147
100.0
src/align/hts/sam/parser.jl

Uncovered Existing Lines

Lines Coverage ∆ File
14
100.0
src/Ragel.jl
Jobs
ID Job ID Ran Files Coverage
1 2213.1 30 Aug 2016 07:06AM UTC 0
81.21
Travis Job 2213.1
2 2213.2 30 Aug 2016 07:05AM UTC 0
81.22
Travis Job 2213.2
4 2213.4 30 Aug 2016 07:17AM UTC 0
81.22
Travis Job 2213.4
Source Files on build 2213
Detailed source file information is not available for this build.
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