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  • MAQ demands pairs have the same length?

    I'm using 0.7.1

    I consistently get one of the two errors when running "maq match" when pairs have different sequence lengths (due to trimming)

    maq: read.cc:61: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strncmp(name, lr->name[j], tl-1) == 0' failed.

    maq: read.cc:58: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `l >= size_r' failed.
    Aborted

    I am forced to set the -1 and -2 options to the shortest sequence in the run. This seems too restrictive to me. What is the logic behind this and why are there separate -1 and -2 options if they have to be set to the same length anyway?
    --
    Jeremy Leipzig
    Bioinformatics Programmer
    --
    My blog
    Twitter

  • #2
    i suspect MAQ might be even more restrictive than I first assumed

    it appears read length cannot vary at all

    is this true?
    --
    Jeremy Leipzig
    Bioinformatics Programmer
    --
    My blog
    Twitter

    Comment


    • #3
      i guess so
      # Is Maq able to deal with reads with variable lengths?

      No and yes. In alignment, all the reads must be in the same length. However, you can `mapmerge' several alignments from reads in different lengths and after that all the subsequent maq commands accept variable lengths.
      --
      Jeremy Leipzig
      Bioinformatics Programmer
      --
      My blog
      Twitter

      Comment


      • #4
        novoalign will do variable read lengths, and has all maq functionality.

        Comment

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