Re: GNU Parallel Bug Reports java flag being interpreted by bash, and 2+ extension chomping

[Andreas Bernauer]

On 21/08/15 19:55, Cameron Prybol wrote:
> an additional problem I have is with the tandem extension dropping
> 
> for example
> ```
> parallel java -jar \
>     $GATK \
>     -T HaplotypeCaller \
>     -R "$REF_DIR/human_g1k_v37.fasta" \
>     -I {} \
>     -dontUseSoftClippedBases \
>     --dbsnp "$REF_DIR/dbsnp_138.b37.vcf" \
>     -stand_call_conf 20 \
>     -stand_emit_conf 20 \
>     -o "$VCF_OUT/"'{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::; =}'.vcf \
>     ::: "$(ls "$BAM_DIR"/*.score_recalibrated.bam)"
> ```
> 
> runs fine with the perl regular expressions in tandem, but anytime I
> want to drop two or more extensions i.e. {/..}, {/...} it fails
> 
> ```
> parallel java -jar \
>     $GATK \
>     -T HaplotypeCaller \
>     -R "$REF_DIR/human_g1k_v37.fasta" \
>     -I {} \
>     -dontUseSoftClippedBases \
>     --dbsnp "$REF_DIR/dbsnp_138.b37.vcf" \
>     -stand_call_conf 20 \
>     -stand_emit_conf 20 \
>     -o "$VCF_OUT/"'{/..}'.vcf \
>     ::: "$(ls "$BAM_DIR"/*.score_recalibrated.bam)"
> ```

I think you have to activate '{/..}' with --plus:

$ echo 'a/b/c/test.1.2' | parallel --plus echo {/..}
test

{= ... =} and {/.} are built-in, though.

-Andreas