bam2chicago.sh breaking in the "Flipping all reads that overlap with the bait on to the right-hand side..."

Issue #77 new
Former user created an issue

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...

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