Reverse complement negative strand reads in fastq output

[arahuja]

Fixes #736

This does slightly differ from Picard. AlignmentRecordConverter currently ignores the negative strand flag is the read is unmapped. That would result in the read not being reverse complemented when output. I've left as is and only compared with Picard on mapped reads.

This then will leave unmapped reads unaltered on output (which seems to be the correct thing to do) but I'm not sure why the aligner would mark it as negative if it was unmapped. I.E. if the aligner reverse complements but then removes the mapping (sets the mapq to 0) perhaps we should look at the flag?

[fnothaft]

License header.

[fnothaft]

Other than a few nits, looks good to me! Thanks @arahuja.

Also, the failing test in Jenkins appears to be org.bdgenomics.adam.cli.Adam2FastqSuite.convert SAM to paired FASTQ. The stack trace is:

java.lang.NullPointerException
      at scala.collection.mutable.ArrayOps$ofRef$.length$extension(ArrayOps.scala:114)
      at scala.collection.mutable.ArrayOps$ofRef.length(ArrayOps.scala:114)
      at scala.collection.SeqLike$class.size(SeqLike.scala:106)
      at scala.collection.mutable.ArrayOps$ofRef.size(ArrayOps.scala:108)
      at scala.collection.mutable.Builder$class.sizeHint(Builder.scala:69)
      at scala.collection.mutable.ArrayBuilder.sizeHint(ArrayBuilder.scala:24)
      at scala.collection.TraversableLike$class.builder$1(TraversableLike.scala:240)
      at scala.collection.TraversableLike$class.map(TraversableLike.scala:243)
      at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108)
      at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:239)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:516)
      at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:513)
      at org.apache.spark.rdd.Timer.time(Timer.scala:57)
      at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:511)
      at org.bdgenomics.adam.cli.Adam2FastqSuite$$anonfun$1.apply$mcV$sp(ADAM2FastqSuite.scala:42)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:97)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
      at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
      at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
      at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
      at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
      at org.scalatest.Transformer.apply(Transformer.scala:22)
      at org.scalatest.Transformer.apply(Transformer.scala:20)
      at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
      at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
      at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
      at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
      at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
      at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)

[arahuja]

Imports and license cleaned up

Test pasts for me locally, but possibly some weirdness in the paths on Jenkins. Updated it, let's see if it works, if not is there somewhere to view the Jenkins page?

[arahuja]

Jenkins, test this please.

[arahuja]

Looks I had to move where the test resources file were, should work now.

[arahuja]

Jenkins, test this please.

[fnothaft]

Merged! Thanks @arahuja.