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walaj / VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules
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`-q` outputs no result #8

Closed die4live closed 8 years ago

die4live commented 8 years ago

I've tried the --qc-file argument with some combination of other args, but in output file, I only got a header 'ReadGroup ReadCount Supplementary Unmapped MateUnmapped QCFailed Duplicate MappingQuality NM InsertSize ClippedBases MeanPhredScore ReadLength' without stats.

Could there be an example for the usage of -q?

walaj commented 8 years ago

Thanks for noticing this. There was a bug where the qc-tracking got commented out. I have updated now. Also, Example 9 now contains a short example of using both the rule-counts flag (-c) and the qc flag (-q).

You may also notice that I overhauled the rules script to now use JSON instead of my custom brew that was becoming onerous to parse. This also has the effect of removing the need for Boost in building. Do let me know if you have any trouble with the new version. Hopefully it should be easier now that rules scripts can be validated using jsonlint.com, and since I added a number of command-line shortcuts that should reduce the need to have to create the JSON script anyway, except for more complex rules combinations.