On 30/05/13 02:43 PM, Rob Egan wrote: > 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. >
Hi Rob, I fixed this. Thank you for the bug report. https://github.com/sebhtml/ray/commit/77270afae197e5f3d422be8e0defc7d79dd55175 > > >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 ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
