Issue #77
new
Hi, this issue as been raised many time, could you fix the bug in bam2chicago.sh line 102:
if($1==$11 && (minRight-maxLeft)/($3-$2)>=0.6){ print $4,$5,$6,$1,$2,$3,$7,$8,$10,$9,$11,$12,$13,$14,$15 }
Bedtools produced files ${samplename}/${bamname}_mappedToBaits.bedpe
has only 14 field but you're printing 15 fields when you enter this conditional. Not sure why it's not breaking for everybody...
Here's the error message I get from line 116:
Command output: Checking rmap and baitmap files... Rmap and baitmap files checked successfully Processing sample DTG-MicroC-138_5000_chinput... Using bam file DTG-MicroC-138-cleanedUp.bam Using baitmap file 5kb.baitmap Using digest map (rmap) file 5kb.rmap Baitmap file contains >4 columns. Checking if 5kb.baitmap_4col.txt exists... It doesn't. So trimming the extra columns and saving the result in 5kb.baitmap_4col.txt... Intersecting with bait fragments (using min overhang of 0.6)... Flipping all reads that overlap with the bait on to the right-hand side... Intersecting with bait fragments again to produce a list of bait-to-bait interactions that can be used separately; note they will also be retained in the main output...