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guanchangge / mosaik-aligner

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Faulty SAM output MosaikText #37

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
Basecalling with Pyrobayes:
---------------------------
1. PyroBayes -i FZGDF8M01.sff -o FZGDF8M01.sff.pyro

Vector & Quality trimming with Figaro and Lucy:
-----------------------------------------------
2. figaro -F FZGDF8M01.sff.pyro.fasta -P clipped.pyro -T 2 -V t
3. figaro_trim_seqs -o trimmed.pyro -f FZGDF8M01.sff.pyro.fasta -q
FZGDF8M01.sff.pyro.fasta.qual  -c clipped.vectorcuts
4. lucy -error 0.025 0.02 -bracket 10 0.02 -window 50 0.08 10 0.3
trimmed.pyro.fasta trimmed.pyro.qual

Aligning with Mosaik:
---------------------
5. MosaikBuild -fr chrX.fa  -ga 18 -oa chrX.fa.dat -sn "Homo Sapiens"
6. MosaikBuild -fr trimmed.pyro.fasta -fq trimmed.pyro.qual  -st 454  -out
trimmed.pyro.fasta.dat
7. MosaikAligner -hs 15 -mm 5 -bw 51 -act 55 -ia chrX.fa.dat -in
trimmed.pyro.fasta.dat -out trimmed.pyro.aligned -p 6
8. MosaikText -in trimmed.pyro.aligned -sam trimmed.pyro.aligned.mosaik.sam

What is the expected output? What do you see instead?

This all happens flawlessly (no errors/warnings given) until I try to
convert the SAM file to BAM with samtools:
Parse error at line 22: sequence and quality are inconsistent
Aborted

When I look at the file at the given line I can see weird non ASCII symbols
and that sometimes the base quality strings contain whitespaces and
carriage returns (which results in the error given above)

What version of the product are you using? On what operating system?

mosaik-aligner 1.0.1388 Linux x64

Please provide any additional information below.

See attach for the first 500 lines of the outputted sam file

Original issue reported on code.google.com by alejandr...@gmail.com on 23 Feb 2010 at 7:56

Attachments:

GoogleCodeExporter commented 8 years ago 
MosaikBuild handles quality values incorrectly when using qual files.

Original comment by WanPing....@gmail.com on 28 Sep 2010 at 8:39

GoogleCodeExporter commented 8 years ago 
The bug has been fixed in version 1.1.0014.

Original comment by WanPing....@gmail.com on 1 Oct 2010 at 8:21