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