index is deprecated

[alexweisberg]

I tried running the make test commands with the newest version of graphtyper (2.6.2, the binary release) and I get the following error:

[lots of text]

Flag meaning:

• D: Discovery iteration.
• G: Genotyping-only iteration.
• V: VCF file was used to initialize the graph.
• |: Iteration separator.
  Academic tradition requires you to cite works you base your article on.
  When using programs that use GNU Parallel to process data for publication
  please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

To silence the citation notice: run 'parallel --citation'.

[GraphTyper's 'index' subcommand deprecated. Graph is now indexed automatically after construction.
parallel: This job failed:
bash /tmp/graphtyper_calling.aIqamQ/call_script.sh /tmp/graphtyper_calling.aIqamQ/config.sh /tmp/graphtyper_calling.aIqamQ/local_bamlist 20:500

This also happens if I try running it with my own dataset.

Also fyi the download link for the binary for the 2.6.2 release is still linking to the 2.5.1 release version.

[hannespetur]

Hello,

The graphtyper subcommands "genotype" and "genotype_sv" replaces these graphtyper pipeline scripts so please use them instead with v2.6.2. The scripts are only still here for reproducibility and since a few publications have references to them. I will add a deprication notice to the README.

Also fyi the download link for the binary for the 2.6.2 release is still linking to the 2.5.1 release version.

Nice catch, thanks for letting me know.

Best,
Hannes