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Feature request #183

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Mohamed-HAMICI opened this issue Mar 19, 2024 · 1 comment · May be fixed by #194
Open

Feature request #183

Mohamed-HAMICI opened this issue Mar 19, 2024 · 1 comment · May be fixed by #194

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@Mohamed-HAMICI
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Hello,

First of all, thank you for this tool that is so easy to use. I am currently using it for the extraction and annotation of BAM files and it works very well.
I thought it may be a good idea if we could have the option to exclude the duplicate reads in the junction count.

Thanks for reading me.
@yfarjoun
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yfarjoun commented Jul 3, 2024

I would like to support this request and expand it to allow a samtools-style -f and -F arguments for required flags and filtered flags

TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
feat: added per-read flag and map quality filtering
409a492 
 - closes griffithlab#183, flag based filtering
 - closes griffithlab#189, mapping quality based filtering
 - option '-F' filters reads containing any of these flags
 - option '-f' filters reads not containing all these flags
 - option '-q' filters reads below this mapping quality
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
feat: added per-read flag and map quality filtering
548b60e 
 - closes griffithlab#183, flag based filtering
 - closes griffithlab#189, mapping quality based filtering
 - option '-F' filters reads containing any of these flags
 - option '-f' filters reads not containing all these flags
 - option '-q' filters reads below this mapping quality
@TimD1 TimD1 linked a pull request Sep 19, 2024 that will close this issue
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@TimD1 TimD1 mentioned this issue Oct 31, 2024
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feat: added per-read flag and map quality filtering fulcrumgenomics/regtools
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@yfarjoun @Mohamed-HAMICI