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NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
https://www.nature.com/articles/s41598-018-23978-z
MIT License
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invalid slice size (ArgumentError) #6

Closed thedam closed 6 years ago

thedam commented 6 years ago

Hi,

the command: /IMSindel/bin/imsindel --bam xxxx.bam --chr chr13 --outd imsRawOuts/ --indelsize 10000 --reffa genome.fa

the error:

>3. considering support reads...done
>4. making consensus seqs from support reads...
Traceback (most recent call last):
    5: from /mnt/ssd_01/PROGRAMS/IMSindel/bin/imsindel:44:in `<main>'
    4: from /mnt/ssd_01/PROGRAMS/IMSindel/lib/ims_indel.rb:31:in `run'
    3: from /mnt/ssd_01/PROGRAMS/IMSindel/lib/ims_indel.rb:87:in `run_make_consensus_support_reads'
    2: from /mnt/ssd_01/PROGRAMS/IMSindel/lib/ims_indel/consensus.rb:34:in `make_support_read_consensus'
    1: from /mnt/ssd_01/PROGRAMS/IMSindel/lib/ims_indel/consensus.rb:78:in `make_consensus_with_threads'
/mnt/ssd_01/PROGRAMS/IMSindel/lib/ims_indel/consensus.rb:78:in `each_slice': invalid slice size (ArgumentError)

(it is relatively small .bam file (137MB))

cheers Damian

holrock commented 6 years ago

hello, I added size check. please update and try. thanks!

thedam commented 6 years ago

works:)