mmp option MosaikAligner

Hi guys,

Is there any difference for the mmp option for MosaikAligner v1.1.0021 and 
v2.1.73?

What I see in the help is pretty different but the results obtained doesn't 
seem so much different.

 v1.1.0021 :
-mmp <threshold>  the threshold # of alignment qualities
(which was described in a published paper as alignment identity cutoff ; is 
this really that?)

v2.1.73
-mmp <threshold>  the percentage of mismatches allowed [0.0 - 1.0]

Here's for one of my samples the % of mapped reads for one sample that I tried 
(it's metagenomics so pretty crazy stuff). I did not make any trimming yet, as 
it was just to test the tool itself.

out.mosaik1.85mmp : 62%
out.mosaik2.85mmp : 62%

With mmp = 0.15, almost anything align.

Command lines for v1.0021
MosaikBuild -q in.fastq.gz -st illumina -out out.mosaik1.85mmp.mkb
MosaikAligner -in out.mosaik1.85mmp.mkb -out out.mosaik1.929ref.85mmp.mka -ia 
ref.dat -j ref_15 -p 12 -a all -m all -hs 15 -mmp 0.85 -minp 0.9 -mhp 100 -act 
20 -bw 29

Command lines for v2.1.73
MosaikBuild -q in.fastq.gz -st illumina -out out.mosaik2.85mmp.mkb 
MosaikAligner -in out.mosaik2.85mmp.mkb -out out.mosaik2.929ref.85mmp.mka -ia 
ref.dat -j ref_15 -p 12 -annpe MOSAIK-2.1.73-binary/2.1.26.pe.100.0065.ann 
-annse MOSAIK-2.1.73-binary/2.1.26.se.100.005.ann -hs 15 -mmp 0.85 -minp 0.9 
-mhp 100 -act 20 -bw 29

I've indexed the reference for each version.

The question is, can you just confirm that the option is the same, even if 
what's written in the help is different.

Thanks a lot for your help.

Original issue reported on code.google.com by jean.chr...@gmail.com on 16 Aug 2013 at 5:20

guanchangge / mosaik-aligner

mmp option MosaikAligner #125