juicer_tools.jar dump creates a dense matrix bigger than the requested limits

[jazberna1]

Are you sure this is a bug? I believe this is a bug, already mentioned here: https://github.com/aidenlab/juicer/issues/132

Describe the bug The juicer juicer_tools.jar dump command seems to create a matrix bigger than the requested limits when used with the -d (dense) flag.

To Reproduce run the example provided in https://github.com/aidenlab/juicer/wiki/Data-Extraction adding the -d flag:

java -jar juicer_tools.jar dump observed KR https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic 1:20480000:40960000 1:20480000:40960000 BP 10000 combined_10Kb.txt -d

Then plotting the resulting matrix combined_10Kb.txt gives the attached jpg where there is a portion of the image surrounding the requested limits.

Expected behavior I expected to get an image restricted to 1:20480000:40960000

Screenshots

Desktop (please complete the following information):

• OS: Red Hat Enterprise Linux Server
• Version 7.5 (Maipo) My Juicer Tools Version is 1.19.02

Additional context Many thanks! Jorge

[sa501428]

I would highly recommend using https://github.com/aidenlab/straw instead of the dump command.