I think you're onto something. I will try to fix the problem as soon as I
get back to a computer.
On Dec 8, 2013 2:10 PM, "John Sullivan" <notifications@github.com> wrote:

> I think your code is shortening the reference sequence you return to be
> the same size as the query sequence, and we end up losing data. Here's some
> debugging output from me putzing around...
>
> name: gi|253409428|ref|GQ227366.1| Influenza A virus (A/pika/Qinghai/BI/2007(H5N1)) segment 1 polymerase PB2 (PB2) gene, complete cds
> score: 39.0
>
> organism.sequence: ATGGAGAGAATAAAGGAATTAAGAGATCTAATGTCACAGTCCCGCACTCGCGAGATACTAACAAAGACCACTGTGGACCATATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTCTCAGAATGAAATGGATGATGGCAATGAAATATCCAATCACAGCGGACAAGAGAATAATAGAGATGATTCCTGAAAGGAATGAACAAGGACAGACACTCTGGAGCAAGACAAATGATGCTGGATCGGACAGGGTGATGGTGTCTCCCCTAGCTGTAACTTGGTGGAATAGGAATGGGCCGACGACAAGTACAGTTCATTATCCAAAGGTTTACAAAACATACTTTGAGAAGGTTGAAAGGTTAAAACATGGAACCTTCGGTCCCGTTCATTTCCGAAACCAAGTTAAAATACGCCGCCGAGTTGATACAAATCCTGGCCATGCAGATCTCAGTGCTAAAGAAGCACAAGATGTCATCATGGAGGTCGTTTTCCCAAATGAAGTGGGAGCTAGAATATTGACTTCAGAGTCACAGTTGACAATAACGAAAGAGAAAAAAGAAGAGCTCCAAGATTGTAAGATTGCTCCCTTAATGGTTGCATACATGTTGGAAAGGGAACTGGTCCGCAAAACCAGATTCCTACCAGTAGCAGGCGGAACAAGCAGTGTGTACATTGAGGTATTGCATTTGACTCAAGGAACCTGCTGGGCACAGATGTACACTCCAGGCGGAGAAGTAAGAAATGACGATGTTGACCAGAGTTTGATCATTGCTGCCAGAAACATTGTTAGGAGAGCAACGGTATCAGCGGATCCACTGGCATCACTGCTGGAGATGTGTCACAGCACACAAATTGGTGGGATAAGGATGGTGGACATCCTTAGGCAAACTCCAACTGAGGAACAAGCTGTGGATATATGCAAAGCAGCAATGGGTCTGAGGATTAGTTCATCCTTTAGCTTTGGAG
>  GCTTCACTTTCAAAAGAACAAGTGGATCATCCGCCACGAAGGAAGAGGAAGTGCTTACAGGCAACCTCCAAACATTGAAAATAAGAGTACATGAGGGGTATGAGGAGTTCACAATGGTTGGGCAGAGGGCAACAGCTATCCTGAGGAAAGCAACTAGAAGGCTGATTCAGTTGATAGTAAGTGGAAGAAACGAACAATCAATCGCTGAGGCAATCATTGTAGCAATGGTGTTCTCACAGGAGGATCGCATGATAAAAGCAGTCCGAGGCGATCTGAATTTCGTAAACAGAGCAAACCAAAGATTAAACCCCATGCATCAACTCCTGAGACATTTTCAAAAGGACGCAAAAGTGCTATTTCAGAATTGGGGAACTGAGCCAATTGATAATGTCATGGGGATGATCGGAATATTACCTGACATGACTCCCAGCACAGAAACGTCACTGAGAGGAGTGAGAGTTAGTAAAATGGGAGTAGATGAGTATTCCAGCACTGAGAGAGTAGTTGTAAGCATTGACCGCTTCTTAAGGGTTCGAGACCAGCGGGGGAACGTACTCTTATCTCCCGAAGAGGTCAGCGAAACCCAGGGAACAGAGAAGTTGACAATAACATATTCATCATCAATGATGTGGGAAATCAACGGTCCTGAGTCAGTGCTTGTTAACACTTACCAATGGATCATTAGAAACTGGGAGACCGTGAAAATTCAGTGGTCTCAGGACCCCACGATGTTGTACAATAAGATGGAGTTTGAACCGTTCCAATCCTTGGTACCTAAAGCTGCCAGAGGTCAATACAGTGGATTTGTGAGAACATTATTCCAACAAATGCGTGACGTACTGGGGACATTTGATACTGTCCAGATAATAAAGCTGCTACCATTTGCAGCAGCCCCACCGAAGCAGAGCAGAATGCAGTTTTCTTCTCTAACTGTGAATGTGAGAGGCTCAGGAATGAGAATACTCATAAGGGGCAATTCCCCTGTGTTCAACTACAA
>  TAAGGCAACCCAAAGACTTACCGTTCTTGGAAAGGACGCAGGTGCATTAACAGAGGATCCAGATGAGGGGACAGCCGGAGTGGAATCTGCAGTACTGAGGGGGTTCCTAATTCTAGGCAAGGAGGACAAAAGATATGGACCAGCATTGAGCATCAATGAACTGAGCAATCTTGCAAAAGGGGAGAAAGCTAATGTGCTGATAGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGTCGAATTGTTTAAAAACGACCTTGTTTCTACT
> reference_alignment: ________________________________________________
>
> query: AGCGAAAGCAGGTCAAATATATTCAATATGGAGAGAATAAAAGAATTAAG
>
> query_alignment: GCGAAAGCAGGTCAAATATATTCAATATGGAGAGAATAAAAGAATTAAG
>