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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Turn terminal deletions into soft clips #7

Closed andreas-wilm closed 8 years ago

andreas-wilm commented 8 years ago

I got a bunch of sequences that get aligned with leading (trailing not observed) deletions e.g. 50D740M1D1M1D2M. Terminal indels don't make sense in an alignment (after all: how do you distinguish between a terminal insertion or deletion?). They should be soft clipped.

isovic commented 8 years ago

That's strange, I thought I had handled this. What parameters are you running GraphMap on?

andreas-wilm commented 8 years ago 
graphmap  -x  illumina

on the previously mentioned 16S database using the official v0.21 and commit e45f9de

andreas-wilm commented 8 years ago

Here's an example sequence: ACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTAGGGGTTGGGGCCTTTGAGGCTTTAGTGGCGCAGCTAACGCGATAAGTAGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCTG

which matches sequence 4453932 with cigar string

50D308M1D114M1I86M1D38M1D9M1I21M1I101M1D8M1I48M1D1M1D2M
andreas-wilm commented 8 years ago

Fixed in dev 604a386. Shall we keep this open until dev is merged on master?

andreas-wilm commented 8 years ago

Merged already? :)

isovic commented 8 years ago

Merged :P