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xjtu-omics / SVision

Detecting genome structural variants with deep learning in single molecule sequencing
GNU General Public License v3.0
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AttributeError: 'pysam.libcalignmentfile.AlignmentFile' object has no attribute 'get_index_statistics' #22

Open tnnandi opened 1 year ago

tnnandi commented 1 year ago

Hi,

I'm using the following version of pysam and getting the error: ref_info = aln_file.get_index_statistics(), AttributeError: 'pysam.libcalignmentfile.AlignmentFile' object has no attribute 'get_index_statistics' when I execute ./SVision -o svision_out/ -b ./supports/HG00733.svision.demo.bam -m ../inputs/svision-cnn-model.ckpt -g ../inputs/hg38.no_alt.fa -n HG00733 -s 5 --graph --qname

pysam 0.11.2.2 py36_1 bioconda

Is there a specific version requirement for pysam?

jiadong324 commented 1 year ago

Please use pysam>=0.19.1.