Weird rectangle output #44
Description
If I run rectangle directly on my epiread it says: "[main_rectangle:79] Error, rectangle cannot cross chromosomes". The manual does not say the input has to be chromosome split.
If I run it on a subset of the epiread in chr1, it finishes but the output looks weird. The output simply appends a 9th column to the epiread file and the 9th column is a string of 1,020,893 Ns.
My epiread input:
1 K00135:125:HFV57BBXX:1:1223:20618:2404 2 - 39154135 C . .
1 K00135:125:HFV57BBXX:1:1223:20618:2404 1 - 39154135 C . .
1 K00135:125:HFV57BBXX:3:2211:8044:44482 1 + 47760131 C . .
1 K00135:125:HFV57BBXX:1:2212:23673:26898 1 - 61731684 CCC . .
1 K00135:125:HFV57BBXX:1:2212:23673:26898 2 - 61731684 CCC . .
1 K00135:125:HFV57BBXX:1:2109:1702:26318 1 - 69191536 TTTCCCC . .
1 K00135:125:HFV57BBXX:3:1109:11759:18599 2 - 173991209 C . .
1 K00135:125:HFV57BBXX:3:1109:11759:18599 1 - 173991209 C . .
My rectangle command-line:
biscuit_0_3_16_linux_amd64 rectangle -o epiread_rslM1Li_chr1_epiread_matrix Mus_musculus.GRCm38.dna_sm.primary_assembly.fa epiread_rslM1Li_chr1.epiread