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thelovelab / tximport

Transcript quantification import for modular pipelines
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Support for new sailfish and salmon formats #9

Closed rob-p closed 8 years ago

rob-p commented 8 years ago

Hi Mike,

This implements (hopefully transparent) support for reading both the new and old Sailfish and Salmon formats. I haven't cut the new release yet, but it corresponds to the beta executable I sent you earlier. Basically, this code just checks if a marker file exists (which is only present when processed with newer version of Sailfish and Salmon). If we're dealing with the new version, it uses an updated reading function and deals with the effective lengths directly. Note: this pull request still doesn't import the effective lengths for older versions of sailfish / salmon yet.

mikelove commented 8 years ago

Thanks! It's great to have the effective length in those files.

I may also try to detect new quant.sf files by the presence of "EffectiveLength" in the header. Stephen Turner pointed out that he (and maybe others) move or rename files https://github.com/mikelove/tximport/issues/5

I'll merge your PR and start hacking in an hour or so

mikelove commented 8 years ago

I tweaked it a bit:

https://github.com/mikelove/tximport/commit/4e2a3b223c1d80f58656879381a194d96ce78281#diff-dd69e134bd79893f01d1fb56280b1ee0R103