add support for cram files

[flokraft85]

Hi,
first of all, paraphase is a really good tool!
It would be great if paraphase could accept cram files as input.

Best,
Florian

[xiao-chen-xc]

Hi @flokraft85 yes we can do that in the next release.

[flokraft85]

Hi @xiao-chen-xc ,
that is fantastic! Thanka a lot.

[xiao-chen-xc]

Hi @flokraft85 Version 3.2 is released and it can support cram files as input.

[flokraft85]

Hi @xiao-chen-xc ,
that is really great! Thanks for adding this feature!

[flokraft85]

Hi @xiao-chen-xc ,
There may still be an issue with how Paraphase handles CRAM files when the location of the reference file (ref.fa) changes relative to the alignment. We run our analysis using a nextflow workflow, meaning that the path to the ref.fa in the CRAM file header points only to the temporary nextflow directory. (/data/work/f7/211d11635b0faded38905bab69fdc7/GRCh38_no_alt_analysis_set_dup_masked.fa).

[E::fai_build3_core] Failed to open the file /data/work/f7/211d11635b0faded38905bab69fdc7/GRCh38_no_alt_analysis_set_dup_masked.fa
[E::refs_load_fai] Failed to open reference file '/data/work/f7/211d11635b0faded38905bab69fdc7/GRCh38_no_alt_analysis_set_dup_masked.fa'
[W::cram_get_ref] Failed to populate reference for id 22
[E::cram_next_slice] Failure to decode slice
ERROR:root:Error running MAGEH1 for sample sample_1...See error message below
Traceback (most recent call last):
  File "/home/humgen/miniconda3/envs/paraphase/lib/python3.10/site-packages/paraphase/paraphase.py", line 148, in process_gene
    bam_realigner.write_realign_bam()
  File "/home/humgen/miniconda3/envs/paraphase/lib/python3.10/site-packages/paraphase/prepare_bam_and_vcf.py", line 102, in write_realign_bam
    for read in wgs.fetch(
  File "pysam/libcalignmentfile.pyx", line 2109, in pysam.libcalignmentfile.IteratorRowRegion.__next__
OSError: truncated file

Hence, paraphase may not have used the ref.fa provided with the "-r" option.

paraphase -b input.cram -o output/paraphase -r ref.fa} -t 40

Best,
FLorian

[xiao-chen-xc]

Hi Florian,

I made some updates. Could you try downloading paraphase-3.2.1a0.tar.gz and install it with pip install paraphase-3.2.1a0.tar.gz? Let me know if this version works in your workflow.

Thanks,
Xiao

[flokraft85]

Hi Xiao,
thanks for the fixing the issue so fast. I tested the 3.2.1 alpha and now everthing works fine!

Best,
Florian

[xiao-chen-xc]

Great! I'll release v3.2.1 soon.