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rtgeval's Issues

Propogate quality scores

Thanks for developing this useful tool.

It would be helpful to propagate call quality information to the "atomized" VCF. This would allow RTG's vcfeval to generate ROC information across the various quality thresholds.

Fail to open the file in hapdip.js for allele evaluation (rtg vcfeval)

Hi Heng,

I would really like to this gives a try, however releases/download/v0.1/rtgevalkit-0.1_x64-linux.tar.bz2 (and the current commit) keep failing on the data-sets I've tried. The weird thing is that the first commands seem to work okay and I made sure all input files exist. The command line in all cases was:

/rtgeval.kit/run-eval -s ref/human_g1k_v37.sdf -b $bed $truth $test

$truth and $test are tabix indexed (bgzipped) vcf files.

The error is as follows:

Running position-based evaluaton (hapdip distEval)...
Normalizing the truth VCF...
Normalizing the test VCF...
Running allele evaluation (rtg vcfeval --squash-ploidy)...
Running allele evaluation (rtg vcfeval)...
./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file
    var file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();
                                                   ^
Error: [File] Fail to open the file
    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)
    at main (./rtgeval.kit/hapdip.js:1636:26)
    at ./rtgeval.kit/hapdip.js:1650:1
./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file
    var file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();
                                                   ^
Error: [File] Fail to open the file
    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)
    at main (./rtgeval.kit/hapdip.js:1636:26)
    at ./rtgeval.kit/hapdip.js:1650:1
./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file
    var file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();
                                                   ^
Error: [File] Fail to open the file
    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)
    at main (./rtgeval.kit/hapdip.js:1636:26)
    at ./rtgeval.kit/hapdip.js:1650:1
./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file
    var file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();
                                                   ^
Error: [File] Fail to open the file
    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)
    at main (./rtgeval.kit/hapdip.js:1636:26)
    at ./rtgeval.kit/hapdip.js:1650:1

Any idea what might be going wrong?

Thanks,
Andreas

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