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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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Insert option for bam2length #3

Closed rpshep closed 3 years ago

rpshep commented 5 years ago

Insert option requires a csv file containing 2 number. Could these be input parameters?

byb121 commented 5 years ago

I think the insert CSV file needs an extra column to say which sample/BAM the stats are for.

The file needs to be checked before starting to process BAM files, to make sure that if given BAM has a corresponding row, otherwise calculate stats on the fly. Currently, it'll just stop working if the number of input BAMs is more than the number of rows in the file. Not sure what'll happen if BAM files are fewer.

keiranmraine commented 5 years ago

What stats are these, read-lengths?

byb121 commented 5 years ago

mean insert size and sd of it. It’s an optional input and does not seem affecting results much, thus I think this issue is at low priority.

keiranmraine commented 3 years ago

Requires file as matched to each input