**Describe the bug
There was a option to specify the snp position file format and output format.
-f Format of SNPs file [ddc1,maf,db,dccq,vcf,torrent,RNA,DNA], Def=dcc1 and
--of Output file format [rows,columns].
we doubt these description is incorrect or ambiguous for coverage mode, if you check the code, coverage mode only support
"tab", "vcf", "gff3" and "gtf"; also not support "--of columns".
To Reproduce
Here we tested "-f" and "--of" and three sets of SNP position file:
SNP position file in txt format with tab delimiter eg. DPYD_97981343_A_C,T chr1 97981343 97981343 A C,T. Below five runs, two failed, three succeed and output the same in column format.
-f txt --of columns: run failed, throw an exception. The reason "txt" is not supported.
-f columns --of columns: run failed, throw an exception. The reason "columns" is not supported.
-f maf --of columns: run failed, throw an exception. The reason "maf" is not supported.
-f vcf --of columns: run failed, throw an exception. The reason is the input is not VCF format.
-f tab --of columns: run succeed.
We use same SNP position file as above but not use "--of" option, and got same results as above
4.SNP position file in MAF format. Both runs succeed and output same.
-f maf --of columns: run failed, throw an exception. The reason "maf" file provides chromosome in "1" but not "chr1"
-f maf --of any: run failed, throw an exception. The reason "maf" file present chromosome with "1" but not "chr1"
SNP position file in VCF formte, below two runs get same output, the "--of" option is ignored.
-f vcf --of columns: run succeeds, the log file shows the input is "vcf" format.
-f vcf --of any: run succeeds, the log file shows the input is "vcf" format.
Expected behavior
"--of columns" not work for coverage mode
"txt" "columns", "maf" is not supported
coverage mode should only support "tab", "vcf", "dccq", "gff3" and "gtf" format, here "dccq" is deprecated, "gff3" and "gtf" are not tested.
Desktop (please complete the following information):
OS: mac or linux
Version : adamajava version 98-0412007c
Additional context
Add any other context about the problem here.
**Describe the bug There was a option to specify the snp position file format and output format.
-f Format of SNPs file [ddc1,maf,db,dccq,vcf,torrent,RNA,DNA], Def=dcc1and--of Output file format [rows,columns].we doubt these description is incorrect or ambiguous for coverage mode, if you check the code, coverage mode only support "tab", "vcf", "gff3" and "gtf"; also not support "--of columns".To Reproduce
Here we tested "-f" and "--of" and three sets of SNP position file:
DPYD_97981343_A_C,T chr1 97981343 97981343 A C,T. Below five runs, two failed, three succeed and output the same in column format.-f txt --of columns: run failed, throw an exception. The reason "txt" is not supported.-f columns --of columns: run failed, throw an exception. The reason "columns" is not supported.-f maf --of columns: run failed, throw an exception. The reason "maf" is not supported.-f vcf --of columns: run failed, throw an exception. The reason is the input is not VCF format.-f tab --of columns: run succeed.4.SNP position file in MAF format. Both runs succeed and output same.
-f maf --of columns: run failed, throw an exception. The reason "maf" file provides chromosome in "1" but not "chr1"-f maf --of any: run failed, throw an exception. The reason "maf" file present chromosome with "1" but not "chr1"-f vcf --of columns: run succeeds, the log file shows the input is "vcf" format.-f vcf --of any: run succeeds, the log file shows the input is "vcf" format.Expected behavior
Desktop (please complete the following information):
Additional context Add any other context about the problem here.