Check why mixed alignment cases are not flagged as error

solgenomics / Bio-GenomeUpdate

Tools for updating a genome assembly

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Check why mixed alignment cases are not flagged as error #23

Closed suryasaha closed 9 years ago

suryasaha commented 9 years ago

Check AlignCoordGroup.pm

sample nucmer output

18361542 18377740 1 16206 16199 16206 99.94 70787664 203766 0.02 7.95 1 1 SL2.50ch03 Contig90
53614018 53614614 17944 17348 597 597 99.66 70787664 203766 0.00 0.29 1 -1 SL2.50ch03 Contig90

500bp.mixedoutoforder.agp.group_coords.stdout

Contig90 SL2.50ch03 18361542 18564072 202530 1 203766 203766 154944 1 1 0 Contains 0 0 48822 0 596 SL2.50ch03:597:53614018:53614614

suryasaha commented 9 years ago

The OUT file is correct

500bp.mixedoutoforder.agp.group_coords.stdout

Contig90 SL2.50ch03 18361542 18564072 202530 1 203766 203766 154944 1 1 0 Contains 0 0 48822 0 596 SL2.50ch03:597:53614018:53614614