najoshi / sickle

Windowed Adaptive Trimming for fastq files using quality
MIT License
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Trimming colorspace reads #23

Open biocyberman opened 10 years ago

biocyberman commented 10 years ago

Hi, I am working with colorspace data. It looks like the following. The problem here is that I may or may not have leading base ('T' or 'G'). In this case I have, and so the length of color string is longer than quality string by 1. The current version if sickle trims and makes them equal in length, which is not desirable in this case. Could you make a quick fix for this?

@Read0001_0 T232220210321032113223303111032211110132102312031313022230113212323232301121 + 6/=622=/?@@228/@=282226;@8=20@@@2/@2///8622/;/=/.@/</8@0///@3@/.-2*/*** @Read00011 T232112302320122200301110131110231202221131132201320022110030112221223320210 + //:@//@?-@@@>/@>.82/@/>;/@=/6@=@/?/6/82;@6//69/228/02>//_/685/50.98-6?//

biocyberman commented 10 years ago

Hi again, I did a hack to make it work for Colorspace. I am doing further testing to be sure.