searchMergedBamsWithSeparator must be set explicitely when using exact sample name match for sample from file extraction.

[dankwart-de]

Unfortunately, the sample extraction is not linked to the file search which results in unexpected behaviour, e.g.:

• You have matchExactSampleNames=true
• But you will get several bam files matching the sample "prefix"

Time for a new metadata model.

[GWarsow]

searchMergedBamWithSeparator has to be set to true in order to work correctly:

bash /icgc/ngs_share/ngsPipelines/RoddyStable/roddy.sh testrun D120.exome@snvCalling HT001 --useconfig=/icgc/dkfzlsdf/analysis/D120/RoddyConfig/applicationProperties2_3.5.5.ini --cvalues='possibleTumorSampleNamePrefixes:( metastasis ),possibleControlSampleNamePrefixes:( control ),selectSampleExtractionMethod:version_2,allowSampleTerminationWithIndex:false,matchExactSampleNames:true,searchMergedBamFilesWithPID:true'

ll -L .../alignment/*
.../alignment/control_HT001_merged.mdup.bam
.../alignment/control_HT001_merged.mdup.bam.bai
.../alignment/metastasis2_HT001_merged.mdup.bam
.../alignment/metastasis2_HT001_merged.mdup.bam.bai
.../alignment/metastasis_HT001_merged.mdup.bam
.../alignment/metastasis_HT001_merged.mdup.bam.bai