ivargr

I also encountered the same problem, both when using the test data and when using other data. I think adding this after line 58 in multigrmpy.py should fix the problem:...

Hi! You are correct, the tar archive seems to be corrupted (maybe the upload was abrupted halfway). I am uploading it again now, but upload time is 4-5 hours. In...

I'm sorry for the mess. Could you try these two again now: http://ivarg.ddns.net/human_pruned_1pc.tar http://ivarg.ddns.net/simulation_data.tar (They are working for me now)

Hi! Sorry, there seems to be a file name missing from the command in the Readme. Can you try this command instead? ``` ../run_benchmark.sh None $simulation_data_dir/hg19_chr1-Y.fa None $graph_dir/wg $simulation_data_dir/haplotype0_only_chr20_no_paths $simulation_data_dir/haplotype1_only_chr20_no_paths...

Thanks for the reply! I'm not sure I fully understand. If I do not have circular genomes, will the simulation then be wrong at the chromosome boundaries? I agree that...

Am I correct that this still is an issue? As far as I can see, sorted_nearest is still using `np.long` here: https://github.com/pyranges/sorted_nearest/blob/master/sorted_nearest/src/clusters.pyx#L11 I get this problem when using pyranges version...

+1 I'm also confused about the same.

Hi! Did you create the index by merging all the chromosome vcfs first? I have created an index by merging the vcfs you shared with me earlier. I have shared...

Hi! The `-r` parameter requires a file ending in something like .fa, .fa.gz, .fq, .fq.gz, fastq, ..etc. So it is failing because it cannot find the extension of the file...

Great, glad to hear :)