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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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SamToPsl adds the flag to the bed name field #38

Closed maximilianh closed 8 years ago

maximilianh commented 8 years ago

this is not documented and I don't see where it makes sense to do this.

lindenb commented 8 years ago

I don't even remember why I wrote this tool :-) , I suppose I wrote this option in the case where the SAM is a secondary/supplementary alignment; it is used to make a difference with the primary alignment.

maximilianh commented 8 years ago

I see. thanks! Maybe it's easier to mark this tool as deprecated and refer people to bedtools?

lindenb commented 8 years ago

that what i wrote in the doc https://github.com/lindenb/jvarkit/wiki/SamToPsl ! :-) I'm going to add a 'deprecated' flag.

Thanks.

maximilianh commented 8 years ago

Wait! I don't think bedtools supports the PSL format. PSL is the only alignment format that I know is useful, apart from SAM...

lindenb commented 8 years ago

ok... ok.. I removed the "deprecated" in the doc..

maximilianh commented 8 years ago

Sorry, yes, didn't realize that this tool is really about PSL.

bedtools is by far not as good, as it removes the whole alignment. the PSL format keeps the whole alignment, and then all the UCSC pslTools can be used (pslFilter, pslReps, pslCdnaFilter, pslSwap, pslCheck, pslScore, pslToChain, pslSort, pslPretty, pslPairs, pslHisto, etc etc)

On Fri, Dec 4, 2015 at 4:54 PM, Pierre Lindenbaum notifications@github.com wrote:

ok... ok.. I removed the "deprecated" in the doc..

— Reply to this email directly or view it on GitHub https://github.com/lindenb/jvarkit/issues/38#issuecomment-162003278.