csort modifies input file

I am trying to use cooler csort (version cooler==0.5.3) without much success. My pairs file pairs.txt has the following format:

chr12   74054834        +       chr17   37101300        -
chr10   107716614       +       chr8    74236985        +
...

and the chromosome size file (hg19_chromsizes.txt):

chr1    249250621
chr10   135534747
...

When I run cooler csort hg19_chromsizes.txt pairs.txt I get the following output:

Enumerating chroms...
chr1	1
chr10	2
chr11	3
chr12	4
chr13	5
chr14	6
chr15	7
chr16	8
chr17	9
chr18	10
chr19	11
chr2	12
chr20	13
chr21	14
chr22	15
chr3	16
chr4	17
chr5	18
chr6	19
chr7	20
chr8	21
chr9	22
chrM	23
chrX	24
chrY	25

and after a few seconds my 14GB contact pairs file is converted into a useless 28 byte binary file, along with a new file pairs.txt.tbi, which I guess it’s the failed attempt to index the former with tabix.

Did I misunderstand the usage of cooler csort? Why does it modify the input file?

Thanks!

[ezorita]

The last version in develop works smoothly. I tried the last commit in master and I wasn’t able to reproduce the input replacement either – the buggy version was the one provided by pip install.

btw, It would be useful to give cooler a version argument in order to ease the debugging process.

Thanks

Eduard

[ezorita]

Indeed 😃

Thanks!