SeqFormatException

[KovachLab]

Hi,

I'm attempting to run sequenceTools to generate pseudo-haploid calls for a list of bamfiles.

However I'm getting the following error:
pileupCaller: SeqFormatException "cannot parse chromosome "

Any suggestions? Thanks!

[stschiff]

Chromosomes are required to be numbered, or be named "MT", "Y" or "X", and they can start with "chr" which gets ignored. This is required because I impose a natural order on chromosomes, which is 1-22,X,Y,MT, so

What are your chromosome names?

[KovachLab]

The chromosome names in the fasta reference are as follows (there are about 8000 scaffolds so I only included a few, their names are all of a similar format) :

LG01
LG02
LG03
LG04
LG05
LG06
LG07
LG08
LG09
LG10
LG11
LG12
LG13
LG14
LG15
LG16
LG17
LG18
LG19
LG20
LG21
LG22
LG23
MT_genome
GmG20150304_scaffold_1408
GmG20150304_scaffold_1409
GmG20150304_scaffold_1410
.
.
.

[stschiff]

OK, this is a problem! I understand this would be great to have, but currently I don't allow this. I strictly operate on a simple chromosomal scale as for humans. The reason is that pileupCaller needs to match up genomic positions (consisting of chromosome name and position in the chromosome) between the incoming pileup data and the provided SNP file. In order for this matching to work faithfully, I work with a strictly ordered list of chromosomes.

I need to think how to best fix this. Perhaps I allow the user to input a custom chromosome/scaffold order, or I simply assume that the chromosomal order is the same in the pileup data and the SNP file.

Sorry, this will take a bit time, and I'm sorry that pileupCaller currently doesn't support scaffolded genomes. Clearly a shortcoming, and I'll work on that.