Respect --exclude-flags 0

[xunjieli]

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]

@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]

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

[xunjieli]

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

The input flag (i.e. --exclude-flag) is passed to pysam for filtering out reads here:

igv-reports/igv_reports/bam.py

Line 47 in b684d69

return pysam.view(*samargs)

Therefore, the reads serialized into data url will respect --exclude-flag. However, because igv-reports isn't setting igv.js options right, igv.js will additionally filter out vendor failed and duplicates.
To respect --exclude-flag, igv-reports needs to turn off all default reads filtering in igv.js and make igv.js display all reads , as the reads being serialized into data urls have gone through filtering (by pysam).

[jrobinso]

If you wish to customize igv options for a track you can do that with the --track-configs option.

[xunjieli]

Ok great. Thanks. That seems to work. For anyone else, the --track-config should look like

[
    {
      "name": "Alignments",
      "url": "path/to/bam.bam",
      "filter": {
        "duplicate": false,
        "vendorFailed": false
      }
    }
]

[jrobinso]

I'm going to reopen as a reminder to allow pass-thru flags to pysam, I was just suggesting --track-config as a workaround.

[jrobinso]

Oh disregard, you can already do that. Sorry for confusion, too many projects.

[jrobinso]

Actually I just understood the logic of this PR, I think your solution is fine. Sorry for my confusion.