java.lang.RuntimeException: Not a diploid organism.

[CornilleAmandine]

Subject of the issue

I got an error message, java.lang.RuntimeException: Not a diploid organism. I am working on a haploid organism. Does that mean that vcf to bam does not work for haploid organism?

Your environment

• version of jvarkit : download on the 9th january 2020
• version of java: java version "1.8.0_112" Java(TM) SE Runtime Environment (build 1.8.0_112-b15) Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)
• the value of /usr/local/public/java
• which OS

Thanks a lot, my best, Amandine

[lindenb]

yes it's only for diploid. I wrote this program for diploid only. If you want to create a 'fake' diploid.

in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java#L288 change the lines:

if(alleles.size()!=2) throw new RuntimeException("Not a diploid organism.");
Allele allele=null;
if(genotype.isPhased())
{
allele =alleles.get(g_strand);
}
else
{
allele = alleles.get(Math.random()< 0.5?0:1);
}

to

Allele allele= alleles.get(0);

and compile again.

(not tested)

[CornilleAmandine]

OK thanks a lot! my best, Amandine

On Sat, 9 Jan 2021 at 13:13, Pierre Lindenbaum notifications@github.com wrote:

yes it's only for diploid. I wrote this program for diploid only. If you want to create a 'fake' diploid.

in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java#L288 change the lines:

if(alleles.size()!=2) throw new RuntimeException("Not a diploid organism."); Allele allele=null; if(genotype.isPhased()) { allele =alleles.get(g_strand); } else { allele = alleles.get(Math.random()< 0.5?0:1); }

to

Allele allele= alleles.get(0);

and compile again.

(not tested)

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