Respect --exclude-flags 0

igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

MIT License

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Respect --exclude-flags 0 #121

Open xunjieli opened 2 weeks ago

xunjieli commented 2 weeks ago

Update tracks.py to set duplicate and vendorFailed in Bam track's options to True. Otherwise, igv.js will filter out duplicate and vendorFailed reads even though --exclude-flags is 0.

Since pysam filters out reads before serializing the data into data url, this PR fixes this bug by making igv.js to show all reads.

xunjieli commented 2 weeks ago

@jrobinso PTAL. To reproduce the bug,

have a few reads that are marked vendorFailed or PCR duplicates.
pass --exclude-filter 0 when creating a report.
Observe that the HTML generated will filter out reads even though user explicitly specified --exclude-filter 0

jrobinso commented 2 weeks ago

I don't understand this change, it looks like you are turning off vendor failed and exclude duplicates flags irrespective of input flags.