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STARSolo add --outBAMsortingBinsN an add a param to force samtools sort #7051

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pavanvidem
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Quick fix to #7043

  • This PR does NOT export --outSAMtype. This patch should still keep the existing functionality of the tool. It adds an extra boolean param use_samtools_sort which forces --outSAMtype BAM Unsorted and uses samtools sort to sort the BAM file.
  • It also exposes --outBAMsortingBinsN and --winAnchorMultimapNmax params which already exist in STAR.

@mvdbeek
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mvdbeek commented Jun 19, 2025

  • It also exposes --outBAMsortingBinsN and --winAnchorMultimapNmax params which already exist in STAR.

I don't think --outBAMsortingBinsN should be a user option, can you calculate reasonable value for that ?

@@ -584,4 +584,30 @@
#end if
]]></token>

<xml name="perf_params">
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There's no way user will set reasonable values here. I would suggest calculating reasonable values for these.

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