Improve sorter. #81
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Improve sorter. #81
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Codecov Report
@@ Coverage Diff @@
## master #81 +/- ##
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+ Coverage 82.42% 83.02% +0.6%
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Files 62 62
Lines 4113 4160 +47
Branches 439 430 -9
=========================================
+ Hits 3390 3454 +64
+ Misses 284 276 -8
+ Partials 439 430 -9
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Oh, I'd totally forgotten about that! 😲 |
totakke
reviewed
Jun 2, 2017
| @@ -131,6 +131,9 @@ | |||
| (def ^:private sort-cli-options | |||
| [["-o" "--order ORDER" "Sorting order of alignments <coordinate|queryname>" | |||
| :default "coordinate"] | |||
| ["-c" "--chunk CHUNK" "Maximum number of alignments sorted per thread." | |||
There was a problem hiding this comment.
Please add [-c CHUNK] to usage line (L142).
"Usage: cljam sort [-o ORDER] [-c CHUNK] <in.bam|sam> <out.bam|sam>"
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@totakke Thank you for the reviewing. I updated usage string in cli. |
totakke
approved these changes
Jun 2, 2017
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Summary
This PR improves functions and performance of
cljam.sorter.Also resolves task 7 in #61.
Changes
sort-by-pos(about 2x faster).sort-by-qname.Affected modules
cljam.sortercljam.bamcljam.samNotes
sort-by-posdoes not checkqname, the same as samtools.