search

biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
Other
8 stars 4 forks source link

filter violation is check twice for the a filter #83

Closed hxin closed 5 years ago

hxin commented 5 years ago

I have tested it with a human sample which ends up the same filtered results before and after the change. So this refactoring does not affect the result. I have made this change in the https://github.com/statbio/Sargasso/commit/c00193150dec8ad24e5207458bd4c809550a621d. This needs to be merged to dev at some point or we can just make the change in dev directly. @lweasel

==> before change ./rna_human_2_enableMultimap_9c37c0bcc9be5b0bfab12611ba4530044ed0d3c7/best/filtered_reads/overall_filtering_summary.txt <== Sample,Assigned-Hits-mouse,Assigned-Reads-mouse,Rejected-Hits-mouse,Rejected-Reads-mouse,Ambiguous-Hits-mouse,Ambiguous-Reads-mouse,Assigned-Hits-rat,Assigned-Reads-rat,Rejected-Hits-rat,Rejected-Reads-rat,Ambiguous-Hits-rat,Ambiguous-Reads-rat,Assigned-Hits-human,Assigned-Reads-human,Rejected-Hits-human,Rejected-Reads-human,Ambiguous-Hits-human,Ambiguous-Reads-human HA1,666470,178348,13460092,5556650,383328,119615,2642336,263985,22176114,5698778,791918,167736,99665728,42296334,13318504,2981202,866668,169800

==> after change Sample,Assigned-Hits-mouse,Assigned-Reads-mouse,Rejected-Hits-mouse,Rejected-Reads-mouse,Ambiguous-Hits-mouse,Ambiguous-Reads-mouse,Assigned-Hits-rat,Assigned-Reads-rat,Rejected-Hits-rat,Rejected-Reads-rat,Ambiguous-Hits-rat,Ambiguous-Reads-rat,Assigned-Hits-human,Assigned-Reads-human,Rejected-Hits-human,Rejected-Reads-human,Ambiguous-Hits-human,Ambiguous-Reads-human HA1,666470,178348,13460092,5556650,383328,119615,2642336,263985,22176114,5698778,791918,167736,99665728,42296334,13318504,2981202,866668,169800

hxin commented 5 years ago

fixed in c41f7f88df32e257127230bdcdecf68614ab6a01