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

[Cameron Prybol]

Hi,

```

$ parallel --version

GNU parallel 20150722

Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange

and Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software: you are free to change and redistribute it.

GNU parallel comes with no warranty.

Web site: http://www.gnu.org/software/parallel

When using programs that use GNU Parallel to process data for publication

please cite as described in 'parallel --bibtex'.

```

I'm having an issue with parallel interpreting a java flag as a file redirect.

running my script

```

$ ./s13.variant_calibration.sh

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

/bin/bash: 2.0: No such file or directory

```

is breaking because of the --filterExpression "QD < 2.0" being interpreted as a < file input in this command

```

parallel java -jar $GATK -T VariantFiltration -R "$REF_DIR/human_g1k_v37.fasta" -V {} -window 35 -cluster 3 --filterName QD --filterExpression "QD < 2.0" --filterName FS --filterExpression "FS > 30.0" -o "$VCF_OUT/"'{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::; =}'.filtered.vcf ::: "$(ls "$VCF_IN"/*.vcf)"

```

I know this because if I change the 

```

--filterExpression "QD < {different value}"

```

to anything besides 2, the error will return

```

/bin/bash: {different value}: No such file or directory

```

(additionally, I have tried several combinations of quotations, \escapes, and changing the flag names of the java program to no avail)

If I drop parallel and just run the java code with hardcoded files (or shell variables), the program runs without error

```

java -jar $GATK -T VariantFiltration -R "$REF_DIR/human_g1k_v37.fasta" -V /users/cjprybol/Parkinsons/VCF/SRR922052.realligned.vcf -window 35 -cluster 3 --filterName QD --filterExpression "QD < 2.0" --filterName FS --filterExpression "FS > 30.0" -o "$VCF_OUT/"SRR922052.filtered.vcf

```

~~~~~

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)"

```

outputs

```

##### ERROR MESSAGE: Couldn't write file /users/cjprybol/Parkinsons/VCF/{/..}.vcf because either the containing directory doesn't exist or it isn't writable

```

however single extension works fine {/.}

parallel has worked fine with 8 other calls I make to the same jar (and another, called Picard), none of which use a < or >, so it seems specific to that IO redirect symbol.

Thanks for making this great tool available!

Best,

Cameron