Considering keeping header line

milkschen / chaintools

Utilities for the genomic chain format

MIT License

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Considering keeping header line #18

Open ebioman opened 8 months ago

ebioman commented 8 months ago

Hello, I had a few chain files today failing when running through some of your tools. Quickly it became evident that header lines are not supported and lead to errors. I was wondering whether there was a particular reason why headers are not accepted? I see that in the UCSC definition headers are not present but some tools generating them (and often the information being stored there being quite useful). Rather a question than an issue ;)

milkschen commented 8 months ago

Hi @ebioman , Thanks for the suggestion. Could you share the link to the tools? I'm happy to take a look at them and support the feature.

ebioman commented 8 months ago

Hi the infamous "axt2chain" from the UCSC tool-chain for example adds information in the header such as:

##gapPenalties=axtChain O=400 E=30
##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chain 22395138222 chr2 242696752 + 3349 242693499 chr2 242193529 + 10324 242182779 1
807     348     0
20864   0       2
5435    0       3
.....