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cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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fragment variable usage is inconsistant #39

Closed keiranmraine closed 5 years ago

keiranmraine commented 5 years ago

$options->{'fragment'} is pulled into a local variable but then a mixture or usage exists. The default is in this file, but also defined as a command line default (after fixing elsewhere).

https://github.com/cancerit/PCAP-core/blob/137acb9379efae21fc3c208320b332f454d47d1f/lib/PCAP/Bwa.pm#L164-L193

Many of the if statements use the options variable, but they indicate values like 5k, the value is in millions and multiplied later so this all needs reviewing.

keiranmraine commented 5 years ago

Also update long form -fragment docs to indicate values >5000 result in no splitting being performed.