#188 fragment names in chimera report file

[schamala]

0-overlaptrim/CeleraRUN.chimera.report file is not showing fragment names in wgs version 6.1-20110830 with bogart option. Output in the chimera report file like below,

intervalHang[2] begGap=210 endGap=210
intervalHang[0] 0,1 interval 13,147 -- overlapregion 13,147 -- 13,147
intervalHang[1] 1,0 interval 178,210 -- 13,147
17 CHIMERA Trimmed from 13 210 to 13 147. Length OK, gatekeeper store updated.
interval[0] = 0-168

[Jason Miller]

Could you provide more information? First, are you running compiled source from the CVS tip? (I ask because release 6.1 did not have a bogart option.) Second, are you after a log with the trim points for every trimmed read? If so, have you tried dumping reports from the gkpStore using the gatekeeper program?

[Brian Walenz]

The logs in OBT (0-overlatrim) will not show the 'names' of the reads, only the assembly-specific ID (the first number on the line). A map from ID to Illumina name can be found in *fastqUIDmap in the assembly directory.