Giter Club home page Giter Club logo

Comments (8)

dpryan79 avatar dpryan79 commented on August 21, 2024 1

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

from methyldackel.

dpryan79 avatar dpryan79 commented on August 21, 2024 1

Thanks for reporting the bug!

from methyldackel.

dpryan79 avatar dpryan79 commented on August 21, 2024

-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.

crazyhottommy avatar crazyhottommy commented on August 21, 2024

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.

dpryan79 avatar dpryan79 commented on August 21, 2024

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.

crazyhottommy avatar crazyhottommy commented on August 21, 2024

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.

crazyhottommy avatar crazyhottommy commented on August 21, 2024

great! thanks for the explaining and user support!

from methyldackel.

dpryan79 avatar dpryan79 commented on August 21, 2024

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

from methyldackel.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.