Export to .hic error #386
Description
Hello!
I'm trying to use TADbit export to convert my matrices to .hic format. When loading the resulting .hic matrices for visualization, I noticed that they looked weird, with bins with higher number of interactions appearing much more intense than usual. I compared the values for the interaction counts, in .abc format and .hic, and noticed that in the case of .hic, a "1" was appended to the beginning of all interaction values, completely distorting the matrices. The remaining characters were more or less the same. When removing that first character, the matrices looked fine again.
Example:
.abc matrix:
0 0 53046542.503318675
0 1 4355693.855483495
0 2 1435752.7571746483
.hic matrix (bins converted to genomic coordinates):
6140000 6140000 153046544.0
6140000 6145000 14355694.0
6140000 6150000 11435753.0
The command I'm using:
tadbit export -w $sample_path --resolution 5000 --format hic -o ../../../2023-02-21-LiftOver_hic_matrices/${sample}_pooled_5kb_hg19.hic \ --bam ${sample_path}/03_filtered_reads/${sample}_capture.bam -c chr12:6140000-8460000 -C 2 -F 1 2 3 9 10 --juicerjar /user/software/juicer/juicer_tools_1.22.01.jar \ --norm --biases $bias_path
I've also tried without the --norm command and the problem persists. I've been loading the .hic matrices with straw. Maybe it's due to some bug in the export function?
Thanks!
Manuel