conversion to stableGaf incorrectly assigns forward orientation

[tobiasrausch]

Hi Heng,

Thanks for pointing out the stableGaf conversion script! When reverse orientation reads align to a single segment (stable sequence), such a GAF line is reduced to PAF (which assumes forward orientation). Here's a script and a single read that reproduces the error:

minigraph --vc -k 15 -w 10 -t 32 -cx lr GRCh38-90c.r518.gfa.gz read.fa > read.vc.gaf
minigraph -k 15 -w 10 -t 32 -cx lr GRCh38-90c.r518.gfa.gz read.fa > read.sq.gaf
mgutils.js stableGaf GRCh38-90c.r518.gfa.gz read.vc.gaf > read.converted.gaf
diff read.sq.gaf read.converted.gaf

>read
GGAACTCTCTGCATGTGCTTCTACGTTCAGTTACGTGTGCTCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGAGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGACCACAGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCTGTCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTTTTGACCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCCTGGCTGGCCTGGCCTGGCCTGGCCTGAGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCCTGGCCCTGGCCCTTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGTACTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGAGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCTCGACGACAGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGCCCTGGCCACAGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGGCATGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCTGCAGCCTGGCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTCGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCCGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGGCCTGGCCTGGCCTGGCCTGGCTGTGGCCTGGCCTGGCTGGCCTGGCCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCCTGGCCTGGCCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCACAGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGACCTCAGCCTGGGCTGGGCCTGAGGCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCTCTGGCCTGGCCCCGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGGCCTGGCCTTGGCCCTTGGCCTGGCCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCTTGGCCTGGCCTAGGCCTAGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCTAGCCCCACAGCCCCAACCCCAGCCCCAGCCCCAGCCCCAACCCCCAGCCCCAGCCCCAAGCCCCAGCCCCAGCCCCAGCCCTACTACAACCCTAGCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAGCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAACCTGCGGCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCGCCTGGCCACCCTGGCCGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCTGGCCGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCAGGCCCTGGCCTGGCCTGGCCCTGGCCCTGGCTGGCCTGGCCTGGCCTGGCCACTGAGCTGGCCTGGCCTGGCCCCGGCGGCCTGGCCTGGCCTGGCCTGGCCTGGCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCACTGGCCGCTGACCGCCCAGCCCCTTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTAGCCCACAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCTGGCCCTGGCCCTGGCCCTGGCCTGGCCTGGCCTGGCCTGGCCTGGCCCTGGCCTAGCCTGGCCCTGGCCTGGCCTGGCCTAGCCCAGCCTAGCCTAGCCTAGCCTAGCCTAACCCTAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAACCCCACTAGCCCCAACCCCAACCCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCCAAACCCCAAACCCTAACCCTAAACCCTAACCCTAACCCTAACCCTAGCCCTAGCCCTAACCCTAACCCTAAACCCTAACCCTAAACCCTAAACCTAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTTACCCTAACCCTAACCCTTAACCCTTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTTACCCCTACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTTAACCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCTAGCCCTCGCCCTCGCCCTCGCCCTCGCCCTCGCCCTCGCCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCTACCTAACCCTAACCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTACAGCAGTACCCTCAACCCGGCCCGCCGCCGGGTCCCTGACCCTGAGGGAGAACTGTCGCTCGCTGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGACAACGCAGCTCCGCCCTCGCGGTGCTCTCCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCGAGCGCAGGCGCAGAGAGCCGCCGCCGCGGCGCCGCGAGCGCAGAGGCGCGCCCGCGCCGCGCAGCGCAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCGCGCCGGCGCAGGCGCAGAGAGGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGGCGCGCGCGCCGGCGCAGGCGCAAGAGAGGCGCGCCGCGCCGACGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCCCGAGGGCGCGGGCGCGCCGGGCCGGCGCAGGCGCGGGGCGCGCCGGGCCGGCGCAGCGCGCCGAGACACACACTCGCTGGCGCGTCCAGGGGAGGAGGCGTGGCACAGGCCGCAGAGACACGTACAGCGCGCCCAGGGGAGGCGTGGCGCAGGGCGCAGAGGGCGTGCGCAGGCGCAGAGACATGCTGGCGCGTCCAGGGGGTGGAGGCGTGGCGCAGGCGCAGAGACGCACGCCTACGGGCAGGGTGGGGAGTACAGGAGCAAGTCGCACGGCGCCGGGCTGGGGGCGGGGG

Thanks, Tobias

[Szhiha]

Could you use the commands above to generate a .gaf file with contents(not empty)?