Merge 1fce868 into 6e6ac8d

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -1558,7 +1558,9 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
               None
             }
           }
-        }).reduce((kv1, kv2) => {
+        }).fold((SequenceDictionary.empty,
+          ReadGroupDictionary.empty,
+          Seq[ProcessingStep]()))((kv1, kv2) => {
           (kv1._1 ++ kv2._1, kv1._2 ++ kv2._2, kv1._3 ++ kv2._3)
         })
 

adam-core/src/test/resources/small.badheader.sam

@@ -0,0 +1,25 @@
+@SQ	SN:1	LN:249250621
+@SQ	SN:2	LN:243199373
+@PG	ID:p1	PN:myProg	CL:"myProg 123"	VN:1.0.0
+@PG	ID:p2	PN:myProg	CL:"myProg 456"	VN:1.0.0	PP:p1
+@RG	ID:badrg	DT:2018-06-27 20:01:02
+simread:1:26472783:false	16	1	26472784	60	75M	*	0	0	GTATAAGAGCAGCCTTATTCCTATTTATAATCAGGGTGAAACACCTGTGCCAATGCCAAGACAGGGGTGCCAAGA	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:240997787:true	0	1	240997788	60	75M	*	0	0	CTTTATTTTTATTTTTAAGGTTTTTTTTGTTTGTTTGTTTTGAGATGGAGTCTCGCTCCACCGCCCAGACTGGAG	*	NM:i:0	AS:i:75	XS:i:39
+simread:1:189606653:true	0	1	189606654	60	75M	*	0	0	TGTATCTTCCTCCCCTGCTGTATGTTTCCTGCCCTCAAACATCACACTCCACGTTCTTCAGCTTTAGGACTTGGA	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:207027738:true	0	1	207027739	60	75M	*	0	0	TTTAATAAATGTTGATTGTCCTATTTAATTATTCTCAACTTTCCGATTTTATTTCCCATGTAACAGTGTTGTTTT	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:14397233:false	16	1	14397234	60	75M	*	0	0	TAAAATGCCCCCATCTTCCCAGAGCTGCCAGCCCTCACAATGCCAACAGCTAAATGTACCCAAGTGTTACTGAAC	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:240344442:true	0	1	240344443	24	75M	*	0	0	TACAGGCACCCACCATCATGCCCAGCTAATTTTTGTATTTTTGTAGAAACGGGGTTTCACCATGTTGGCCCAGCT	*	NM:i:0	AS:i:75	XS:i:61
+simread:1:153978724:false	16	1	153978725	60	75M	*	0	0	GCTCACTGCAGCCTCAACCTCCTGGGCCCAAGTGATTTCATCTTATTTTTGGAAAAAAAAACAAACTAAACCAAA	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:237728409:true	0	1	237728410	28	75M	*	0	0	TTTCTTTTTCTTTCTTTCTTTCTTTCTTTCTTTTTCTTTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCT	*	NM:i:0	AS:i:75	XS:i:59
+simread:1:231911906:false	16	1	231911907	60	75M	*	0	0	TCATGTAGCATGCATATGGCTAACGGCAAAGTGAGGGAGGAATAATTATAGTAATAATCACAGTGATGACGTGGA	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:50683371:false	16	1	50683372	60	75M	*	0	0	GCTCAGGCCTTGCAAGAATCTCTACTGCCCAACAAGTCCCTACAAGATGGCATTTAAAAGCAGTCCCTCACGCAC	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:37577445:false	16	1	37577446	60	75M	*	0	0	CCTAGAGAAGCTCCCACTAGGGCTGCAGTCAATTCCCAGGTCTTAGGTGCTGAGCAGTGGGAGGTGGTGGCCATG	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:195211965:false	16	1	195211966	60	75M	*	0	0	AAATAAAGTTTGGCTTTCAGTTGTAACTTTGAATATCTTTATCACAGTTATTTAAAGCCTTTAAAAAGCTTTAAT	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:163841413:false	16	1	163841414	60	75M	*	0	0	TGTGTAACTAACATAATTGGCACTGTCCCTGTAAATTCAAATTGGATATCCTCCCAAATTTTATTTAAGCAATTG	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:101556378:false	16	1	101556379	60	75M	*	0	0	TTTATTTTTTGAGCATGAAAGTAATATATGCTCAGTGTAAACAATTAGGTCATTATAAATATATTTAACAGGAAT	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:20101800:true	0	1	20101801	35	75M	*	0	0	CTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGACTACAGGCATGAGGCACCGCGCCTGGCCAGGACT	*	NM:i:0	AS:i:75	XS:i:55
+simread:1:186794283:true	0	1	186794284	60	75M	*	0	0	GACAAGATAGTACTTGAGCTAAGCCTTGCAGGTTGAGTAGGATTATTCTAGTGGAATTTAGGGAAACGATGTGCA	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:165341382:true	0	1	165341383	60	75M	*	0	0	CTACTCTCATTGACTGTTCAATGCCTATACAAGTAAAACTTTACCAGCACCCAAGTCAAAAAGAAAAAAAAGGGG	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:5469106:true	0	1	5469107	60	75M	*	0	0	CTCATTCTCTCTCCTGCTGCACTGTGAAGAGGTGCCTGTTGCCAAGAGTATAAGTTTCCTGAGGCCTCCCAGGCC	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:89554252:false	16	1	89554253	60	75M	*	0	0	AAATTAAACAGCTCGTTTAACTGATAATCCATACTATATTTGAGTAGGGCTGTCACATGGTTGGAACCTCCGGTT	*	NM:i:0	AS:i:75	XS:i:0
+simread:1:169801933:true	0	1	169801934	40	75M	*	0	0	AGACTGGGTCTCACTATGTTGCCTAGGCTGGTCTCAAACTCCTGGGCTCAAGTGATCCATCTCTGCCTTCCAAAG	*	NM:i:0	AS:i:75	XS:i:52

adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala

@@ -98,6 +98,14 @@ class ADAMContextSuite extends ADAMFunSuite {
     assert(reads.dataset.rdd.count === 20)
   }
 
+  sparkTest("can read a small .SAM file with a bad header with lenient validation") {
+    val path = testFile("small.badheader.sam")
+    val reads = sc.loadAlignments(path, stringency = ValidationStringency.SILENT)
+    assert(reads.rdd.count() === 20)
+    assert(reads.dataset.count === 20)
+    assert(reads.dataset.rdd.count === 20)
+  }
+
   sparkTest("loading a sam file with a bad header and strict stringency should fail") {
     val path = testFile("badheader.sam")
     intercept[SAMFormatException] {