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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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sga-bam2de.pl: Use DistanceEst -l30 #143

Closed sjackman closed 6 years ago

sjackman commented 6 years ago

Use DistanceEst -l30 rather than -l100. The default minimum alignment score of BWA-MEM is 30, and so also 30 bp in length for a perfect match.

Fix the following error, which occurs when there's a contig that is smaller than the minimum alignment length.

DistanceEst: MLE.cpp:180: int maximumLikelihoodEstimate(unsigned int, int, int, const std::vector<int>&, const PMF&, unsigned int, unsigned int, bool, unsigned int&): Assertion `len1 >= l' failed.
Aborted

Fixes #142.

sjackman commented 6 years ago

For comparison, the default value of l for ABySS is 40, a minimum alignment score and length of 40 bp with abyss-map. See https://github.com/bcgsc/abyss/blob/master/bin/abyss-pe#L263

jts commented 6 years ago

Thanks, I appreciate the patch.

sjackman commented 6 years ago

No worries at all, Jared.