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
