Error in cosmic_format_index.pl with absolute paths

[lpalomerol]

Hello, I've been trying to run this perl program and I've found one error when running it using absoblute paths

This is the command I've performed:

perl /home/idibell/opt/ISOWN/bin/cosmic_format_index.pl \ ~/opt/ISOWN/external_databases/CosmicCodingMuts.vcf.gz \ ~/opt/ISOWN/external_databases/CosmicNonCodingVariants.vcf.gz

The error appears at combine headers step and is a "file not found error", this is the error trace:

"Combine headers ...cat: **_/home/idibell/opt/ISOWN/external_databases/CosmicCodingMuts.vcf.gz.header:** No existe el fichero o el directorio cat: _/home/idibell/opt/ISOWN/external_databases/CosmicNonCodingVariants.vcf.gz.header: No existe el fichero o el directorio "

I've checked the code and the origin of this error are the zcat outputs, you are adding an underscore in the begin of the file location, and chrashes when the file is an absolute path

`

printf "\nExtract headers from ${CODING_FILE} and ${NON_CODING_FILE} ...";

system "zcat $CODINGFILE | head -500 | grep \"^#\" | grep -v CHROM > ${CODING_FILE}.header";

system "zcat $NON_CODINGFILE | head -500 | grep \"^#\" > ${NON_CODING_FILE}.header"; `

Regards, Luis.

[qtrinh]

Hi Luis We have updated cosmic_format_index.pl to support absolute path. Thanks for letting us know.

Q

[lpalomerol]

You are welcome!