Bug: hg19.lastdb and hg19.seq.dict hardcoded in callSV.pm

[wdecoster]

Hi,

I received the following output and error from LongRead.sh:

real    40m3.389s
user    352m16.314s
sys     2m24.308s

Genome sequence fasta file is needed for homopolymer detection only.
Lastal database dictionary 'hg19.seq.dict' does not exist. 
/home/wdecoster/bin/Picky-0.2.a/src/picky.pl callSV --in <alignFile> --fastq <fqFile> --lastpara <last parameters> [--genome <genomeFastaFile> --removehomopolymerdeletion] [--sam] [--exlucde <chromosomeToExeclude> [--exlucde <anotherChromosomeToExeclude>]]

  --oprefix STR   prefix for output files
  --fastq STR     .fastq file
  --lastpara STR  lastal parameters used
  --removehomopolymerdeletion
                  exclude DEL and INDEL possibly affected by homopolymer
  --genome STR    genome sequence in .fasta file
  --sam           flag to output .sam file
  --exclude STR   exclude SV invovling specified chromosome
                  (specify each chromosome with --exclude individually)
  --multiloci     report SVs on best alignment of multi-loci aligments

real    0m0.559s
user    0m0.363s
sys     0m0.195s
Processing NA19240_guppy1.4.0_training_set.profile.DEL.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.INS.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.INDEL.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.INV.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.TTLC.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.TDSR.xls.. 1.. done.
Processing NA19240_guppy1.4.0_training_set.profile.TDC.xls.. 1.. done.

It turns out 'hg19.lastdb' is hardcoded in the callSV.pm module, line 185.

my $pg_db = 'hg19.lastdb';

If I understood correctly, from this also the name 'hg19.seq.dict' is derived in line 271-272 of callSV.pm

On my system, these files do not necessarily exist.

Cheers,
Wouter