On 31.07.2014 17:26, Alec Wysoker wrote: > See the Picard FAQ: > > http://sourceforge.net/p/picard/wiki/Main_Page/#q-why-am-i-getting-errors-from-picard-like-mapq-should-be-0-for-unmapped-read-or-cigar-should-have-zero-elements-for-unmapped-read > > -Alec >
Well, that shows that it is known behavior of PicardTools, but still, is it *correct* behavior given the format specifications ? > On 7/31/14, 4:36 AM, Wolfgang Maier wrote: >> Hi, >> >> I've tried to run SamToFastq on a sam file with unaligned reads. Right >> on the first line picardtools complains: >> >> Exception in thread "main" >> htsjdk.samtools.SAMFormatException: Error parsing text SAM >> file. MAPQ must be zero if RNAME is not specified; Line 4 >> Line: >> HWI-EA332_1_2_662_117/1 4 * 0 255 * * >> 0 0 >> CCACACTACACCCTAACACACCCTAATCTAACCCTGGCCAACCTGTCTCTC >> BBBBCCCCBB@BCB?CBC@ABB?<>AB?CBCBB@BC>BB@BB7BCB<BCA? RG:Z:007 >> >> After consulting the sam format specifications I think that this >> behavior is incorrect. >> The read has bit 4 set in the FLAG field and with that "no assumption >> can be made about RNAME, POS, CIGAR, MAPQ", so picard shouldn't even >> look at MAPQ here. >> Even if it did, I don't know whether it should expect MAPQ to be zero in >> the absence of RNAME as a MAPQ value of 255 "indicates that the mapping >> quality is not available", which seems to be about as reasonable as >> setting it to 0. >> >> Please correct me if I'm getting this wrong, >> Wolfgang >> >> >> ------------------------------------------------------------------------------ >> Infragistics Professional >> Build stunning WinForms apps today! >> Reboot your WinForms applications with our WinForms controls. >> Build a bridge from your legacy apps to the future. >> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk >> _______________________________________________ >> Samtools-help mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/samtools-help > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
