Hyphenated character handling igblast pipelines.

Issue #4 wontfix
Roy Jiang created an issue

Igblast seems to dislike gap characters. Unclear how this affects the ultimate output from igblast.

START> igblastn VERSION> igblast 1.6.1, build Oct 25 2016 15:05:43 IGDATA> /ysm-gpfs/pi/kleinstein/oconnor_abseq/reference/igblast_db GERMDB> imgt_human FILE> SR_Norm-unique.fasta

PROGRESS> [Running] CFastaReader: Hyphens are invalid and will be ignored around line 5154

[rj265@c23n10 RQ2410_A7VEF_2014-04-2]$ awk 'NR==5154' SR_Norm-unique.fasta ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCACGAACTCCGGCCGGCCCTCCAGGGAAGATGGCCACCACGTCGCCCGGCGCGAAGCCCAGCTGGCGGAAGAGGTTGGCTACCGCATTGGAGTAGGCGTCCAGCTGCGCAAAGGTCCAGCACTCGCCGGTCCCGGCATCCACCAGCGCCAGGCGCTCGGGCTGTCGCTGCACTACCGCCTGAAAGATGCGCGGGATGGTGTGGCCGGCACGCTGGTGCCGCCGCAGCTCCAGGCGCACGCGGATCAGCACAGAGAGACCGAAGAGGTCTCGCCTCGCGGTCTTGCAGACGATGCGCAGGAAGCGCCAGCCGCCGCTGCCCACGTACGCGCCGGGCGCCGCTGCCGCGCTCCAGGTCCACGGCAGCCCCAGCAGCCACAACAGCGCCAGCGAGACCACCGAGGCCGCGCCCGCACCCGGAGCCCGCATCCTGGGGAAGCAGAGGGAGCTGAGGCCGCGGGCCGCTCCAGCCCCGCCCCACC

Comments (1)

  1. Log in to comment