AG try debugging w extend #1
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…tAussie/GERMLINE into ag-try-debugging-w-extend
… when answers are inconsistent
adonomay
changed the base branch from
master
to
ag-version-1-5-1-from-columbia-germline
adonomay
changed the base branch from
ag-version-1-5-1-from-columbia-germline
to
master
svohr
reviewed
May 15, 2018
ajsams
reviewed
May 15, 2018
| @@ -90,7 +95,7 @@ int main(int argc, char* argv[]) | |||
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| GERMLINE germline; | |||
| germline.mine( params ); | |||
| return 1; | |||
| return 0; | |||
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There's a spot in the pipeline where I remember we were handling this bug, so we'll need to fix that.
ajsams
reviewed
May 15, 2018
| { | ||
| if ( node[0]->getChromosome( a )->getMarkerSet()->getMarkerBits()[cur_marker] != node[1]->getChromosome( b )->getMarkerSet()->getMarkerBits()[cur_marker] ) | ||
| err = true; | ||
| found_mismatch = true; // err may actually mean end-of-homozygous-tract? |
ajsams
reviewed
May 15, 2018
| * `germline -haploid -w_extend -bits 41` (or any bits value > 1) now produces correct match tracts | ||
| * exit codes follow shell-script convention: 1 for error, 0 for success | ||
| * `germline -version` now reports the version number | ||
| * added tests |
ajsams
approved these changes
May 15, 2018
|
@svohr the one change was passing the marker_set_number parameter to the getMarkerSet function call in lines 85 and 86 of Match.cpp |
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needs testing of haploid and homoz-only -w_extend with multiple dogs.
Edit: have tested this in bulk on dobermans and ref panel v7, looks good (eCOI is consistent with measured COI)