Need help to read in the mcool file converted by hicexplorer
zhjilin opened this issue · 1 comments
Hi,
Has anyone come across problems to read the mcool files converted by hicexplorer? Not sure what went wrong, can someone give some hints where should I change in mcool?
Thanks!
First, I figured out there should be "format-version" attribute in mcool file, so I added it back "format-version: 2". (I guess it should be 2. I tried 1 and 3, didn't read either)
However, it threw the following error:
output=CreateBrick_from_mcool(Brick="./test40k", binsize=40000, mcool="Merged.4bins_corrected.mcool", remove.existing=T)
Error in rep(chr, Offset) : invalid 'times' argument
Here I listed the file content, one from my file and the other one from the example:
h5ls("Merged.4bins_corrected.mcool")
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 40000 H5I_GROUP
2 /resolutions/40000 bins H5I_GROUP
3 /resolutions/40000/bins chrom H5I_DATASET ENUM 27752
4 /resolutions/40000/bins end H5I_DATASET INTEGER 27752
5 /resolutions/40000/bins start H5I_DATASET INTEGER 27752
6 /resolutions/40000/bins weight H5I_DATASET FLOAT 27752
7 /resolutions/40000 chroms H5I_GROUP
8 /resolutions/40000/chroms length H5I_DATASET INTEGER 32
9 /resolutions/40000/chroms name H5I_DATASET STRING 32
10 /resolutions/40000 indexes H5I_GROUP
11 /resolutions/40000/indexes bin1_offset H5I_DATASET INTEGER 27753
12 /resolutions/40000/indexes chrom_offset H5I_DATASET INTEGER 33
13 /resolutions/40000 pixels H5I_GROUP
14 /resolutions/40000/pixels bin1_id H5I_DATASET INTEGER 81274286
15 /resolutions/40000/pixels bin2_id H5I_DATASET INTEGER 81274286
16 /resolutions/40000/pixels count H5I_DATASET FLOAT 81274286
h5ls("../4DNFI7JNCNFB.mcool")
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 1000 H5I_GROUP
2 /resolutions/1000 bins H5I_GROUP
3 /resolutions/1000/bins KR H5I_DATASET FLOAT 3088281
4 /resolutions/1000/bins VC H5I_DATASET FLOAT 3088281
5 /resolutions/1000/bins VC_SQRT H5I_DATASET FLOAT 3088281
6 /resolutions/1000/bins chrom H5I_DATASET ENUM 3088281
7 /resolutions/1000/bins end H5I_DATASET INTEGER 3088281
8 /resolutions/1000/bins start H5I_DATASET INTEGER 3088281
9 /resolutions/1000/bins weight H5I_DATASET FLOAT 3088281
10 /resolutions/1000 chroms H5I_GROUP
11 /resolutions/1000/chroms length H5I_DATASET INTEGER 24
12 /resolutions/1000/chroms name H5I_DATASET STRING 24
13 /resolutions/1000 indexes H5I_GROUP
14 /resolutions/1000/indexes bin1_offset H5I_DATASET INTEGER 3088282
15 /resolutions/1000/indexes chrom_offset H5I_DATASET INTEGER 25
16 /resolutions/1000 pixels H5I_GROUP
17 /resolutions/1000/pixels bin1_id H5I_DATASET INTEGER 356526446
18 /resolutions/1000/pixels bin2_id H5I_DATASET INTEGER 356526446
19 /resolutions/1000/pixels count H5I_DATASET INTEGER 356526446
20 /resolutions 10000 H5I_GROUP
21 /resolutions/10000 bins H5I_GROUP
22 /resolutions/10000/bins KR H5I_DATASET FLOAT 308837
23 /resolutions/10000/bins VC H5I_DATASET FLOAT 308837
Hi,
Sorry for the very long silence on this thread. I haven't had the chance to take a look at the repository for quiet some time. HiCExplorer and sparse format files are a planned addition for bioconductor release 3.11.
Other than that, I am trying to find the source of your bug. Can you please provide a file for testing purposes?