Reorganize BAM I/O #97
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Codecov Report
@@ Coverage Diff @@
## master #97 +/- ##
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+ Coverage 83.86% 84.87% +1%
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Files 60 60
Lines 4122 3953 -169
Branches 430 399 -31
========================================
- Hits 3457 3355 -102
+ Misses 235 199 -36
+ Partials 430 399 -31
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Slow tests of $ lein clean
$ lein test :only cljam.algo.t-sorter
Reflection warning, pathetic/core.clj:264:14 - reference to field getPath can't be resolved.
Reflection warning, pathetic/core.clj:265:18 - call to method lastIndexOf on java.lang.String can't be resolved (argument types: unknown).
Reflection warning, clj_http/lite/core.clj:75:7 - call to method setChunkedStreamingMode on java.net.URLConnection can't be resolved (no such method).
lein test cljam.algo.t-sorter # hangs up on this line |
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Thank you for the comment. It finishes but is slower than the master because of a bug. 🙇 |
totakke
reviewed
Aug 17, 2017
- Remove :depth option for read-alignments. Now it returns SAMAlignments only. - partially decoded alignments are available with read-blocks. - Reading functions return Eduction instances instead of lazy sequences. - Fix read-blocks to check end positions. - Use records for reading blocks. - Implemented LSBWritable to remove duplicated codes in cljam.io.bam.writer and cljam.io.bam.encoder. - Avoid reflections.
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Thanks! I amended the commit message with some comments. |
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Perfect, thank you! |
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Thank you for reviewing! |
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summary
Overall refactoring and some API changes of BAM module, including performance improvements.
changes
:depthoption forread-alignments. Now it returnsSAMAlignments only.read-blocks.Eductioninstances instead of lazy sequences.read-blocksto check end positions.cljam.io.bam.writerandcljam.io.bam.encoder.and some cosmetic changes.
tests
lein test :all🆗benchmarks
This PR slightly affects the performance of lots of tasks.
Here're some benchmarks compared to
[cljam "0.4.1"].environment
results
4394ms3494ms8247ms7799ms7360ms5503ms7918ms7848ms1018ms1025ms