--keepDupes and -F 0x400 gives me different results about methyldackel HOT 8 CLOSED

-F 0xB00 rather than multiple -F values, but otherwise yes. I'll make that the default in the next bug fix version.

from methyldackel.

Thanks for reporting the bug!

from methyldackel.

-F 0x400 is exactly the opposite of --keepDupes. -F in MethylDackel is the same as -F in samtools view, so you're then instructing it to ignore duplicates (but then include secondary and supplemental alignments, since you've overridden the default value of 0xF00 or 3840).

from methyldackel.

Thanks. so, If I need to include the duplicates, I can do:

MethylDackel --keepDupes

# or

MethylDackel -F 0x100 -F 0x200 -F 0x800

what if one uses both --keepDupes and -F together? and the order of the flag also matters seems.

e.g. This seems to give different results.

MethylDackel -F 0x400  --keepDupes
MethylDackel   --keepDupes -F 0x400

Thanks,
Tommy

from methyldackel.

The -F option is processed first when reads are filtered, so if you filter it then --keepDupes is ignored. This looks like a bug, actually, since I'm now not sure that --keepDupes is properly doing anything since it isn't changing the -F default. I think I should change the -F default to 0xB00, I'll have to test that.

from methyldackel.

Thanks for the detail. I just tested

MethylDackel -F 0x100 -F 0x200 -F0x800
MethylDackel   --keepDupes  -F 0x100 -F 0x200 -F0x800

I thought these two are the same. -F 0x100 -F 0x200 -F0x800 will keep the duplicates, but one needs to specify --keepDupes as well for the counting.

For my purpose, I will need to do to keep the duplicates but discarding failed qc, secondary and supplementary reads:

MethylDackel   --keepDupes  -F 0x100 -F 0x200 -F0x800

right?

Thanks,
Tommy

from methyldackel.

great! thanks for the explaining and user support!

from methyldackel.

Sorry for the delay on this, it's now fixed in the 0.4.0 release.

from methyldackel.