Rational args

docs/MANUAL.md

@@ -587,6 +587,8 @@ You can also test them individually by running:
     % (cd test-data; make test-scenario6)
     % (cd test-data; make test-long-template)
     % (cd test-data; make test-paired-end)
+    % (cd test-data; make test-demultiplexed)
+    % (cd test-data; make test-demultiplexed-paired-end)
 
 ## Recommended JVM Settings
 
@@ -632,7 +634,7 @@ command-line options:
       --col-reference <file>   reference file for column barcodes (i.e., conditions)
       --umi-reference <file>
       --global-reference <file>
-      --row-reads <files>      required if reads are split between two files
+      --row-reads <files>      required if reads are split between two files or for demultiplexed data
       --rev-row-reads <files>  required for processing paired-end sequencing data
       --col-reads <files>      required if reads are split between two files
       --reads <files>          required if reads are contained in a single file

project/build.properties

@@ -1 +1 @@
-sbt.version=1.9.4
+sbt.version=1.9.6

src/main/scala/org/broadinstitute/gpp/poolq3/PoolQConfig.scala

@@ -39,10 +39,12 @@ final case class PoolQInput(
   def readsSourceE: Either[Exception, ReadsSource] = (rowReads, reverseRowReads, colReads, reads, demultiplexed) match {
     case (None, None, None, Some(r), false) =>
       Right(ReadsSource.SelfContained(Nel(r._2, addlReads.view.map(_._2).toList)))
+
     case (Some(rr), None, Some(cr), None, false) =>
       val rs = ReadsSource.Split(Nel(cr, addlColReads), Nel(rr._2, addlRowReads.view.map(_._2).toList))
       if (rs.forward.length == rs.index.length) Right(rs)
       else Left(PoolQException("Number of row, column, and reverse reads files must match"))
+
     case (Some(rr), Some(rrr), Some(cr), None, false) =>
       val rs = ReadsSource.PairedEnd(
         Nel(cr, addlColReads),
@@ -51,12 +53,15 @@ final case class PoolQInput(
       )
       if (rs.forward.length == rs.index.length && rs.forward.length == rs.reverse.length) Right(rs)
       else Left(PoolQException("Number of row and column reads files must match"))
-    case (None, None, None, Some(r), true) =>
-      Right(ReadsSource.Dmuxed(Nel(r, addlReads)))
+
+    case (Some(rr), None, None, None, true) =>
+      Right(ReadsSource.Dmuxed(Nel(rr, addlRowReads)))
+
     case (Some(rr), Some(rrr), None, None, true) =>
       val rs = ReadsSource.DmuxedPairedEnd(Nel(rr, addlRowReads), Nel(rrr, addlReverseRowReads))
       if (rs.read1.map(_._1) == rs.read2.map(_._1)) Right(rs)
       else Left(PoolQException("Row and column reads files must match"))
+
     case _ => Left(PoolQException("Conflicting input options"))
   }
 
@@ -170,7 +175,7 @@ object PoolQConfig {
         val _ = opt[List[(Option[String], Path)]]("row-reads")
           .valueName("<files>")
           .action { case (ps, c) => c.copy(input = c.input.copy(rowReads = ps.headOption, addlRowReads = ps.drop(1))) }
-          .text("required if reads are split between two files")
+          .text("required if reads are split between two files or for demultiplexed data")
           .validate(_.view.map(_._2).toList.traverse_(existsAndIsReadable))
 
         val _ = opt[List[(Option[String], Path)]]("rev-row-reads")

test-data/Makefile

@@ -191,7 +191,7 @@ test-demultiplexed:
 	--col-reference $(conditions) \
 	--row-reference $(reference) \
 	--demultiplexed \
-	--reads TTGAACCG:../../test-data/demultiplexed/TTGAACCG.construct.fastq,CCGAGTTA:../../test-data/demultiplexed/CCGAGTTA.construct.fastq,TTGAGTAT:../../test-data/demultiplexed/TTGAGTAT.construct.fastq,CCTCCAAT:../../test-data/demultiplexed/CCTCCAAT.construct.fastq,GGTCACCG:../../test-data/demultiplexed/GGTCACCG.construct.fastq,TTGACAAT:../../test-data/demultiplexed/TTGACAAT.construct.fastq,AATCCAAT:../../test-data/demultiplexed/AATCCAAT.construct.fastq,TTCTCATA:../../test-data/demultiplexed/TTCTCATA.construct.fastq,AATCCACG:../../test-data/demultiplexed/AATCCACG.construct.fastq,AATCGTGC:../../test-data/demultiplexed/AATCGTGC.construct.fastq,AAGAACTA:../../test-data/demultiplexed/AAGAACTA.construct.fastq,CCAGTGAT:../../test-data/demultiplexed/CCAGTGAT.construct.fastq,GGTCGTGC:../../test-data/demultiplexed/GGTCGTGC.construct.fastq,TTAGACCG:../../test-data/demultiplexed/TTAGACCG.construct.fastq,GGTCCACG:../../test-data/demultiplexed/GGTCCACG.construct.fastq,CCGAACTA:../../test-data/demultiplexed/CCGAACTA.construct.fastq,AACTCACG:../../test-data/demultiplexed/AACTCACG.construct.fastq,AATCACTA:../../test-data/demultiplexed/AATCACTA.construct.fastq,GGTCCATA:../../test-data/demultiplexed/GGTCCATA.construct.fastq,GGTCTGCG:../../test-data/demultiplexed/GGTCTGCG.construct.fastq,CCAGTGGC:../../test-data/demultiplexed/CCAGTGGC.construct.fastq,AACTTGCG:../../test-data/demultiplexed/AACTTGCG.construct.fastq,../../test-data/demultiplexed/unmatched.construct.fastq \
+	--row-reads TTGAACCG:../../test-data/demultiplexed/TTGAACCG.construct.fastq,CCGAGTTA:../../test-data/demultiplexed/CCGAGTTA.construct.fastq,TTGAGTAT:../../test-data/demultiplexed/TTGAGTAT.construct.fastq,CCTCCAAT:../../test-data/demultiplexed/CCTCCAAT.construct.fastq,GGTCACCG:../../test-data/demultiplexed/GGTCACCG.construct.fastq,TTGACAAT:../../test-data/demultiplexed/TTGACAAT.construct.fastq,AATCCAAT:../../test-data/demultiplexed/AATCCAAT.construct.fastq,TTCTCATA:../../test-data/demultiplexed/TTCTCATA.construct.fastq,AATCCACG:../../test-data/demultiplexed/AATCCACG.construct.fastq,AATCGTGC:../../test-data/demultiplexed/AATCGTGC.construct.fastq,AAGAACTA:../../test-data/demultiplexed/AAGAACTA.construct.fastq,CCAGTGAT:../../test-data/demultiplexed/CCAGTGAT.construct.fastq,GGTCGTGC:../../test-data/demultiplexed/GGTCGTGC.construct.fastq,TTAGACCG:../../test-data/demultiplexed/TTAGACCG.construct.fastq,GGTCCACG:../../test-data/demultiplexed/GGTCCACG.construct.fastq,CCGAACTA:../../test-data/demultiplexed/CCGAACTA.construct.fastq,AACTCACG:../../test-data/demultiplexed/AACTCACG.construct.fastq,AATCACTA:../../test-data/demultiplexed/AATCACTA.construct.fastq,GGTCCATA:../../test-data/demultiplexed/GGTCCATA.construct.fastq,GGTCTGCG:../../test-data/demultiplexed/GGTCTGCG.construct.fastq,CCAGTGGC:../../test-data/demultiplexed/CCAGTGGC.construct.fastq,AACTTGCG:../../test-data/demultiplexed/AACTTGCG.construct.fastq,../../test-data/demultiplexed/unmatched.construct.fastq \
 	--row-barcode-policy PREFIX:CACCG@18)
 	(cd $(wd); diff counts.txt ../../test-data/expected-counts.txt && \
      diff lognormalized-counts.txt ../../test-data/lognormalized-counts.txt && \