Step 6 breaks with underscore in chromosome names.

[aakashsur]

It looks like step 6 breaks with underscores in chromosome names as well.

It can be isolated to:

mHiC/mhic_step0-6.sh

Line 172 in 0e5c13a

awk -v OFS="_" '{print $2, $3, $4, $5}' $multi | sort -u >$multiKeys

mHiC/s6_em_cython.pyx

Line 94 in 0e5c13a

pair = pairString.rstrip().split("_")

mHiC/s6_em_cython.pyx

Line 153 in 0e5c13a

pair = "_".join([pairLine[1], pairLine[2], pairLine[3], pairLine[4]])

mHiC/s6_em_cython.pyx

Line 184 in 0e5c13a

pair = "_".join([pairLine[0], pairLine[1], pairLine[2], pairLine[3]])

mHiC/s6_em_cython.pyx

Line 291 in 0e5c13a

position = "\t".join(pairKeys[alignPair[j]].strip().split("_"))

[yezhengSTAT]

Yes, again we assume the chromosome name has no underscore and is consistent for the whole processing procedure.