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fixes for cluster

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akmorrow13 committed May 10, 2019
1 parent 9ea49cf commit 2a6dfbaaa6dc79a7f5b26f9b0deca8aa54755b60
@@ -4,12 +4,7 @@
<%@ val genes: Option[String] %>
<%@ val reads: Option[List[String]] %>
<%@ val variants: Option[Map[String, String]] %> <!-- map of file name and samples to extract genotype ids/names -->
<%@ val features: Option[List[(String, Boolean)]] %> <!-- if true, then the track should be a coverage track -->
<%@ val region: ReferenceRegion %>

<%@ val reads: Option[List[String]] %>
<%@ val variants: Option[Map[String, String]] %> <!-- map of file name and samples to extract genotype ids/names -->
<%@ val features: Option[List[(String, Boolean)]] %> <!-- if true, then the track should be a coverage track -->
<%@ val features: Option[Map[String, Boolean]] %> <!-- if true, then the track should be a coverage track -->
<%@ val region: ReferenceRegion %>

<html xmlns="http://www.w3.org/1999/html">
@@ -171,7 +171,7 @@ object BamReader extends GenomicReader[SAMFileHeader, AlignmentRecord, Alignment
try {
sc.loadIndexedBam(fp, predicateRegions, stringency = ValidationStringency.SILENT)
} catch {
case e: java.lang.IllegalArgumentException => {
case e: Exception => { // IllegalArgumentException if local or FileNotFoundException if hdfs
log.warn(e.getMessage)
log.warn("No bam index detected. File loading will be slow...")
sc.loadBam(fp, stringency = ValidationStringency.SILENT).filterByOverlappingRegions(predicateRegions)

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