Commit 2309ce61 authored by M. Haseeb's avatar M. Haseeb

ENA-3842

- fixed an issue that ran cram specific processing steps on bam files causing null pointer errors.
parent 9425069e
Pipeline #92127 passed with stages
in 2 minutes and 52 seconds
......@@ -21,7 +21,7 @@ wrapper{
group = 'uk.ac.ebi.ena'
ext.version_base = '1.2.0'
ext.version_base = '1.2.1'
version = version_base
sourceCompatibility = '1.8'
targetCompatibility = '1.8'
......
......@@ -201,7 +201,11 @@ implements Validator<ReadsManifest, ReadsValidationResponse>
try
{
fileResult.add(ValidationMessage.info("Processing file"));
scanner.readCramFile( fileResult, rf, paired );
if (rf.getFiletype().equals(Filetype.cram)) {
scanner.readCramFile( fileResult, rf, paired );
} else {
scanner.readBamFile( fileResult, rf, paired );
}
} catch( SAMFormatException | CRAMException ex )
{
......
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