Can't load index file for cram file

[ChristinaXu2017]

According to GitHub issues #33 and #34. the latest CNVnator can read CRAM files. Yes, it can read the CRAM file but not the CRAM index file. I got below error message: Can't load index file for '/path/test.cram'.

The command line I used is

export REF_PATH=/reference/g/GRCh37_ICGC_standard_v2.fa;
./cnvnator -pe /path/test.cram -qual 40 -over 0.8 -root /path/test.rawresults.root  -f /path/test.rawresults.tsv 

The index file is created by samtools and renamed to

• /path/test.cram.crai;
• /path/test.cram.bai;
• /path/test.crai;
• /path/test.bai.

I doubt the error occurs on AliParser.cpp

  if (loadIndex) {
      index = bam_index_load(fileName.c_str());
      if (!index) cerr<<"Can't load index file for '"<<fileName<<"'."<<endl;
    }

[ChristinaXu2017]

it can't load cram file, unless Change index file handle from bamidx to hts_idx_t on AliParser.*.

• AliParser.hh hts_idx_t *index; //bam_index_t *index;

• AliParser.cpp

if (loadIndex) {
    //index = bam_index_load(fileName.c_str());
    samFile *hts = sam_open(fileName.c_str());
     index = sam_index_load2( hts, fileName.c_str(), NULL);
     ...

The reason is

• bam_index_load() defined inside htslib/sam.h, can’t take cram file
• sam_index_load(fp,fn) defined inside htslib/sam.h can process cram file
• htslib/sam.h::sam_index_load(fp,fn) calls sam_index_load2( fp, fn, NULL), so here we use sam_index_load2 to process cram file

[abyzov]

Hi, thanks for the info. Perhaps, it would be better to switch to CNVpytor (https://github.com/abyzovlab/CNVpytor) as it is better maintained.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 7-91 Rochester, MN 55905 www.abyzovlab.org tel: +1-(507)-538-0978

[ChristinaXu2017]

thanks, will try it.