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medvedevgroup / TwoPaCo

A fast constructor of the compressed de Bruijn graph from many genomes
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gfa1 Format issue (path orientation) #8

Closed ChriKub closed 7 years ago

ChriKub commented 7 years ago

Hi,

the pats in the gfa1 dumped by graphdump seem to have a wrong format. For some of the segments in the path the the orientation is missing and for all segments that have one the orientation is given before the segment number instead of after (although I'm not sure if this is an actual error or if it is allowed based on the format specification) Output: P seq1_repeat_seq2_seq3 -23,17,-31,27,-8 31M,31M,31M,31M gfa spec example: P 14 11+,12-,13+ 4M,5M

Is this the correct format or is there something wrong? Thanks, Chris

iminkin commented 7 years ago

That is probably a bug, I will make a minor release. Thanks for pointing that out.

iminkin commented 7 years ago

Fixed in 0.9.2.