Execute HTSJDK In Non-Strict Mode

[DarioS]

Could an example of how to make HTSJDK run non-strictly be added to the user guide? For TCGA whole genome sequencing, different centres used different versions of hg19 with a different number of contigs. This causes an exception like

INFO	2019-09-30 02:43:41	TwoBitBufferedReferenceSequenceFile	Caching reference genome contig 22
[Mon Sep 30 02:44:13 AEST 2019] gridss.SoftClipsToSplitReads done. Elapsed time: 16.12 minutes.
Runtime.totalMemory()=4052221952
Exception in thread "main" java.lang.IllegalArgumentException: Reference index for 'NC_007605' not found in sequence dictionary.

In HTSJDK, it comes from

            if (NO_ALIGNMENT_REFERENCE_INDEX == referenceIndex) {

                if (strict) {

                    throw new IllegalArgumentException("Reference index for '" + referenceName + "' not found in sequence dictionary.");

                }

Indeed, the BAM file doesn't have an SQ entry for that contig (sample processed by Baylor College of Medicine), but the FASTA file (provided by Broad Institute) does have a record for it.

I don't care much about chromosomes other than 1, 2, 3, …., X, Y, MT, so I hope that when I run GRIDSS, I can force HTSJDK to ignore these discrepancies by specifying a simple option.

[d-cameron]

You'll need to add VALIDATION_STRINGENCY=LENIENT or VALIDATION_STRINGENCY=SILENT to the java calls in the driver script.

--picardoptions pass-through option added to driver script: e.g.

 ../scripts/gridss.sh --picardoptions "COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT"  -t 4 -b wgEncodeDacMapabilityConsensusExcludable.bed -r ../hg19.fa -w out -o out/gridss.full.chr12.1527326.DEL1024.vcf -a out/gridss.full.chr12.1527326.DEL1024.assembly.bam -j ../target/gridss-2.6.2-gridss-jar-with-dependencies.jar --jvmheap 8g chr12.1527326.DEL1024.bam