[ADAM-1697] Expand Illumina metadata regex to cover interleaved index sequences.

adam-core/src/main/java/org/bdgenomics/adam/io/InterleavedFastqInputFormat.java

@@ -58,7 +58,7 @@ public final class InterleavedFastqInputFormat extends FastqInputFormat {
      */
     private static class InterleavedFastqRecordReader extends FastqRecordReader {
 
-        private final String firstReadSuffix = ".+([/ +_]1| 1:[YN]:[02468]+:[0-9]+)$";
+        private final String firstReadSuffix = ".+([/ +_]1| 1:[YN]:[02468]+:[0-9ACTG]+)$";
         private Pattern firstReadRegex;
 
         InterleavedFastqRecordReader(final Configuration conf,

adam-core/src/test/resources/read_names_with_index_sequences_interleaved.fq

@@ -0,0 +1,32 @@
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1116:2123 1:N:0:ATCACG
+TCTGTGTAAATTACCCAGCCTCACGTATTCCTTTAGAGCAATGCAAAACAGACTAGACAAAAGGCTTTTAAAAGTCTAATCTGAGATTCCTGACCAAATGT
++
+CCCFFFFFHHHHHJJJJJJJJJJJJHIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJHIJGHJIJJIJJJJJHHHHHHHFFFFFFFEDDEEEEDDDDDDDDD
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1116:2123 2:N:0:ATCACG
+NTAATAATGAGTGCACAATAGTTTTTCTCCTGAAACATAATTATTCTCTCAATCATCCCCATCCCCACCAAAGTCAATCACGGGAAGATCAATCAGCCTGC
++
+#1=DFFFFHHHFHIJJIIIJJJIJJJIJJJJJJJIJJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJIJIJIJJHHHHHHHFFFDDDDDDDDDDDDDDDDDD
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1129:2182 1:N:0:ATCACG
+AAGCTGACTTGTGTTGGGAGCTCATCTGTTCCCTTGACTTCTCTTTTTCCAGTTCTTCGTCAAGGCCACAGGTGCTGCGGGAAAATCAGTAACTAATGAAC
++
+@C@FFFDFFFDFBHGDHH;EHHGHE?EBHCHIGGI>BFFECGGIIIIGIHEBBGCHHIG);;FEEADGH<ACAEDDBCCCBBCCCBCCC>@CCDCCC@CCC
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1129:2182 2:N:0:ATCACG
+TCCTCCCACTTCTGTCTCCCTCAGCAGCCTCTCATATTGCTGCTGTCTGCCTGGCCTATAGGCTTCTGAGTTATGACACTGGTGTGAAGAGAAAAGGCTTN
++
+1?@DABDDDDF+AE?EBFHIIII>G>?;8?3?EEF<FF9@<DFGDD9?D93?BD889=)=<C3=C)=7DAD77=?7?A:EB2?96;@DB@?=;>B;5<5(:
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1158:2217 1:N:0:ATCACG
+AGCTGACATGAGAAAAGCCTGGTAAATCCGGGGCAAGTGACTGAAATGAAAGAATCCAATCAGATTCCAGCTCCAAGGGCCGCTAATTGTAGTAACTGGCT
++
+CCCFDFFFHFFFFGIIGGHJEB<CEFIJJIIIHGECG9BFDHGGIGHJFHIGEHHIIAHHGGEEFDDDFDBCEDECCBB@5=BDDDDEC:>@DDEDE@>??
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1158:2217 2:N:0:ATCACG
+ATATTAAGCCACTTGCAGCAAGACAGCCTGAAACTTCGTGACTCCCTGGAGCTTTTGGTGGTGGACGAAGCTGACCTTCTTTTTTCCTTTGGCTTTGANNN
++
+C@CFDFFFHGHGHIJJJIGHHHIJJJIIEHIJJJJJIHDFGBFGIIJGGHIGIJJGEHCFH@EHEEEDFCDCDDDDDDDDDDDDDDDDDDCDDCDDCDDCC
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1499:2087 1:N:0:ATCACG
+TCATTCCACATCTCAATCTCTCCTAGGAAGTTTTCCGGCCTTGTTGACAGGTTTAATTGAAAGGAGAAGCCAAATGTTGAGTAAACAGATTGCAAAAACTG
++
+CCCFFFFFHHFHHJJJJJIJIIJHJJJJJJIIJIJJGIIIIJIJJJJJJJJBFIIJJJJJJJJJJJJJJHHHHHFF?DFFFEEEEEEDDCDDDDDDDDDDC
+@HISEQ_HU01:89:H7YRLADXX:1:1101:1499:2087 2:N:0:ATCACG
+NNNNNNNNNNNNNNNNNNNNNGGATAANNANCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++
+#####################22@@??##1#0############.############################################++8::<======

adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala

@@ -577,7 +577,7 @@ class FragmentRDDSuite extends ADAMFunSuite {
     checkSave(variantContexts)
   }
 
-  sparkTest("Paired read names with index sequences in read names can grouped into fragments") {
+  sparkTest("paired read names with index sequences in read names can group into fragments") {
     val path1 = testFile("read_names_with_index_sequences_pair1.fq")
     val path2 = testFile("read_names_with_index_sequences_pair2.fq")
     val fragments = sc.loadPairedFastq(path1, path2).toFragments()
@@ -588,4 +588,26 @@ class FragmentRDDSuite extends ADAMFunSuite {
       assert(fragment.getAlignments.size() == 2)
     })
   }
+
+  sparkTest("interleaved paired read names with index sequences in read names can group into fragments") {
+    val path = testFile("read_names_with_index_sequences_interleaved.fq")
+    val fragments = sc.loadInterleavedFastq(path).toFragments()
+
+    assert(fragments.rdd.count() == 4)
+
+    fragments.rdd.collect().foreach(fragment => {
+      assert(fragment.getAlignments.size() == 2)
+    })
+  }
+
+  sparkTest("interleaved paired read names with index sequences in read names as fragments") {
+    val path = testFile("read_names_with_index_sequences_interleaved.fq")
+    val fragments = sc.loadInterleavedFastqAsFragments(path)
+
+    assert(fragments.rdd.count() == 4)
+
+    fragments.rdd.collect().foreach(fragment => {
+      assert(fragment.getAlignments.size() == 2)
+    })
+  }
 }