virus-evolution/gofasta

Issues

• Unsupported chars in reference id? and accepting GFF3 filename extension

  #44 opened 9 months ago by mmokrejs
  3

• Accept --offset argument to adjust the nuc/aa positions

  #46 opened 9 months ago by mmokrejs
  2

• --reference sometimes accepts filename and sometimes chrID

  #45 opened 9 months ago by mmokrejs
  2

• Question: Does gofasta ignore SNPs in the first 16 nt of a sequence?

  #49 opened 9 months ago by mmokrejs
  1

• panic: runtime error: index out of range [29899] with length 29899

  #41 opened 2 years ago by Xiang-Leo
  7

• Error: empty fasta file

  #38 opened 2 years ago by Jinke233
  1

• Handle I/O errors gracefully

  #22 opened 2 years ago by benjamincjackson
  0

• node distances for updown

  #19 opened 2 years ago by benjamincjackson
  2

• consolidate fastaio functions

  #16 opened 2 years ago by benjamincjackson
  0

• increase the test coverage

  #12 opened 2 years ago by benjamincjackson
  0

• annotation features from reverse strand

  #37 opened 2 years ago by fifthguy
  7

• gofasta snps -> open : no such file or directory

  #9 opened 4 years ago by tseemann
  2

• How does closest measure IUPAC codes?

  #32 opened 2 years ago by tseemann
  1

• Better error message for variants

  #30 opened 2 years ago by benjamincjackson
  0

• extend genbank parsing / mutation annotation to protein products

  #23 opened 2 years ago by benjamincjackson
  3

• What should the coordinate system be for sam indels?

  #20 opened 2 years ago by benjamincjackson
  0

• Support for max-dist in 'closest' command

  #31 opened 3 years ago by tseemann
  3

• Mutation missing from output

  #28 opened 3 years ago by mattdmem
  5

• sam indels doesn't read from stdin

  #17 opened 3 years ago by benjamincjackson
  0

• skip secondary mappings in sam indels

  #14 opened 3 years ago by benjamincjackson
  0

• possible bug in gofasta sam toMultiAlign

  #21 opened 3 years ago by rmcolq
  8

• updown --reference flag help inaccurate

  #15 opened 3 years ago by benjamincjackson
  0

• external licences in the binary

  #11 opened 3 years ago by benjamincjackson
  1

• What are the flags for sam toMultiAlign

  #5 opened 4 years ago by josephhughes
  1