thegenemyers/DAZZ_DB — pull request #4 by pbjd (2014-09-11 00:09:17+00:00)
Title: fasta2DB: Skip subreads with ranges greater than 2^16

Ran into this while integrating with HGAP. When casting int's to ushorts with subreads ranges larger than 2^16 corrupts beg/end values in the record buffer. A side effect of this is that the pbid in the DB becomes corrupted, creating a book-keeping issue in HGAP. Here are some examples found in my dataset:

>m131021_044647_42175_c100583802550000001823087704281485_s1_p0/95966/47433_65693
>m131023_015910_42175_c100583712550000001823087704281400_s1_p0/76055/59571_70914
>m131023_015910_42175_c100583712550000001823087704281400_s1_p0/117753/66441_69466

I put in a simple fix to just skip subreads that fall in this category and emit a warning.