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cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
http://cancerit.github.io/cgpPindel/
GNU Affero General Public License v3.0
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Possible to generate more records than input pairs #73

Closed keiranmraine closed 5 years ago

keiranmraine commented 5 years ago

Stats in error stream can appear wrong due to potential for both reads in a pair to generate a record, e.g.

Thread Worker 1282: Excluded -218352/500000 (1588s)
Thread Worker 1282: Generated 718352 records

Due to the initial count being based on pairs, instead of reads, while the returned value is records generated. Changing total_pairs to total_reads will resolve this apparent negative count:

https://github.com/cancerit/cgpPindel/blob/f196e69c966bfccd52029dc0953f84f17c28aa8a/perl/lib/Sanger/CGP/Pindel/InputGen.pm#L244-L248

keiranmraine commented 5 years ago

Fixed in 31089fcd2f26faff470cd8330a0c11d41b50bae0