Read Names are Trimmed

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I'm aligning SOLiD paired reads.  The forward (F3) reads are 50 long, while the 
reverse (F5-P2) reads are 35 long.  Can Mosaik handle paired reads of different 
lengths?

My paired read names look like this:
>4_37_1284_1
>4_37_1284_2

Afterwards, the read names have been trimmed:
4_37_128
4_37_128

Even after specifying '-tpr 0 -tsr 0' within MosaikBuild, my read names are 
still trimmed.  Why does this happen?

Thank you,
Simon.

Original issue reported on code.google.com by simon.ch...@gmail.com on 25 Jan 2011 at 12:03

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What steps will reproduce the problem?
1.  MosaikBuild -fr F3.csfasta -fr2 F5-P2.csfasta -fq F3.qual -fq2 F5-P2.qual 
-out ReadArchive.dat -st solid -tpr 0 -tsr 0
2.  MosaikAligner -ia cs_hg18.dat -ibs bs_hg18.dat -in ReadArchive.dat -hs 15 
-mm 6 -mhp 100 -act 20 -j Jump_Database -p 6 -out Aligned.dat -rur 
unaligned.fastq
3.  The unaligned.fastq file contains the trimmed read names as described above

What is the expected output? What do you see instead?
I expect to see the same read names in my original csfasta file, but in my 
unaligned.fastq file, the read names have been trimmed.

What version of the product are you using? On what operating system?
Mosaik version 1.1.0021

Original comment by simon.ch...@gmail.com on 25 Jan 2011 at 12:10