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AlignmentRecordMaterialization fails with sam files (no index) #322

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akmorrow13 opened this issue Oct 16, 2017 · 0 comments
Open

AlignmentRecordMaterialization fails with sam files (no index) #322

akmorrow13 opened this issue Oct 16, 2017 · 0 comments
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0.0.6

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@akmorrow13
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org.bdgenomics.mango.models.UnsupportedFileException: bam index not provided for file /data/chr17.7500000-7515000.sam. Stack trace: java.lang.IllegalArgumentException: requirement failed: Did not find any files at /data/chr17.7500000-7515000.sam.
at scala.Predef$.require(Predef.scala:224)
at org.bdgenomics.adam.rdd.ADAMContext.loadIndexedBam(ADAMContext.scala:633)
at org.bdgenomics.mango.models.AlignmentRecordMaterialization$$anonfun$loadFromBam$1.apply(AlignmentRecordMaterialization.scala:189)
at org.bdgenomics.mango.models.AlignmentRecordMaterialization$$anonfun$loadFromBam$1.apply(AlignmentRecordMaterialization.scala:181)
@akmorrow13 akmorrow13 added this to TODO in 0.0.6 Nov 8, 2019
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