Misc improvements before index optimisation PR

iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads

MIT License

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Closed leoisl closed 11 months ago

leoisl commented 11 months ago

This PR contains several misc small fixes:

Fixes a segfault bug with getting the wrong pangraph node, introduced in the previous PR;
Fixes a minor bug that caused unmapped reads to be suppressed in the file SAM;
Removes the --clean command line option, redundant now that gene-DBGs code were removed;
Adds CLI option --rng-seed to make multimapping deterministic, if required;
A handful of clean ups of unused code;

leoisl commented 11 months ago

@mbhall88 feel free to comment on this, I can still incorporate changes