Anyone used Segemehl aligner?

[lbragg]

Just FYI -- a patch for this version has fixed the output to give correct SAM output. Hoorah!

[lbragg]

I'm referring to this alignment software: http://www.bioinf.uni-leipzig.de/Software/segemehl/, which was published in PLoS Comp. Bio (http://www.ploscompbiol.org/article/...l.pcbi.1000502).

I really want to get this set up in a workflow, as I am interested in both mismatches and insertions/deletions (I am using 454 reads).

Problem is, I can't find any documentation about the output format. The number of column headers doesn't match the number of columns in the results, and some of the rows don't actually correspond to the headers. In addition, I'm not sure how the 'meop string' works, I thought it was a SAM formatted alignment, but I am seeing softing clipping internally, which I thought was not valid in SAM format.
eg.

M1;I1;S8;M1;S8;M1;S18;M1;S2;M1;S5;M3;S3;M1;S2;M1;S1;M1;

The paper has been cited 41 times, so someone has definitely worked this out before! I have contacted the authors, but I thought in the meantime that I might be able to get some help from the seq answers forum.

Thanks in advance!