Hello Sebastien,
When using some of the scaffolds from Ray, I noticed that sometimes the
format of the file is improperly folded. Whenever a gap between contigs of
the scaffold lands exactly at column 60, the subsequent N's are continued
on that same line instead of on the following line, leaving a 120 character
line. Below is a snippet example. This formatting problem breaks some code
like samtools faidx.
>scaffold-7
GTCGACTTCCTCGGCCTTGCTCCAGATCGGCGTCTTCACCGCGCCCGGCGCGATGACGAT
GACATCGATGCCGAACAGCATCATTTCGCGGCGCAGGCTTTCCGAAAGTCCCTCGATCGC
GTGCTTCGATGCCGAATAGGCCGACATCAGGGGGTTGCCGTTTTTGCCGGCCACCGAACT
GATCATCACGATCCGCCCCCGTGGTCCCTTCAGCGACGGATCGGATCCGAGCAGCGGACC
GAAGGCTTGGGTGGCGATGATCGGCCCGACGACGTTCACATCCATCTGGCGACGGAATTC
GTCGGCCGCGAGCTCGAGCACCGGCCCGGCGACCGCGATGCCGGCATTGTTGACGAGGCC
AAAGAGCGCCTCGCCACCCAGCGCGGCGCGGACCTCGCGAGCGGCTGCGAGCACCGCGGC
CTCATCGGTGACATCGAACAGCAGCGGCGTAAAATTCGCGCCGAATTCGCTCTTCAGGCG
GTCGGCATCAGCCTGCTTGCGCACGCTGCCGAACACACGGAAACCGCGATCGAGCAGTAG
CTTCGCGGTGGCCCAGCCGATGCCGGTGGACGCTCCGGTGATGACAACAGATTGCATGGT
TGAAATTCCTCTCCGAACGATTTTTTTGCGCTCAGCGCGGAAAACGCTGATCCCCCGCTT
GCTCGGCTGCGCATGATATCACGCGCCGGCGGGTTCTACCCGTGCTTGTGACACCCAGGT
CCGGTAAAGCCGGGTGCGCCGCTTGGTGAGGATCTGCTGGCGGATCAATGCCAACAGTGG
ACTGGCGTCAGGTTTCGGCCGCTTGCCTTTGCCGAGGCGGCGCAGTTGCAGCTTCACCAG
CGCCATCCTCGCAAGGCTTGCATAGGCCTTGTTGCGCCAGCCGACGCTCGGCATTTCGAT
ATCGAGTGCTTCGCCGCCCTTCCACCGTTCGGGCAGCTTCGGCTCGAACGCCATGGCGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNAATGCCAACAGTGGACTGGCGTCAGGTTTCGGCCGCTTGCCTTTGCCGAGG
CGGCGCAGTTGCAGCTTCACCAGCGCCATCCTCGCAAGGCTTGCATAGGCCTTGTTGCGC
CAGCCGACGCTCGGCATTTCGATATCGAGTGCTTCGCCGCCCTTCCACCGTTCGGGCAGC
TTTGGCTCGAACACCATGGCGCTGGCGATGCCGACCATGGCGACCCCCGGCCTGCCCTCG
TCTGGCTTCAGCGCCTGCTCGGCGACGGCGCGCCGGCGGATACCGCCCGTGACCATGACC
GGCATCCGCGCAACTGCGCTGATGTCGCGCGCGAAATCGAGAAAATAAGCTTCGCGCACG
GCGGTGCTGCCGGCCTGCGGCGCGCCTTGCATGGCCGGGCTTTCGTAGCTGCCACCGGAC
AATTCCACGAGATCGACCGGCAACTCGTTGAGCCAGCGCACCACCTGCACGGCGTCCGAC
I suspect that there is an off-by-one bug in the scaffold fasta output code.
Thanks,
Rob Egan
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