Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:

-- Picard extension so Queue scripts can use FastqToSam
-- Single-sample BAM processing: merge/trim reads + BWA + IR + MD + BQSR. Mostly identical to standard pipeline,
except for the adaptor trimming/merging which is critical for short-insert libraries.
-- Single-sample calling (experimental, work in progress): standard UG run but outputting at all sites, meant for
deep whole genomes.

New scripts

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala

@@ -0,0 +1,104 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.queue.extensions.picard
+
+/*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+import org.broadinstitute.sting.commandline._
+
+import java.io.File
+
+class FastqToSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction /*with PicardBamFunction*/ {
+  analysisName = "FastqToSam"
+  javaMainClass = "net.sf.picard.sam.FastqToSam"
+
+  @Input(shortName = "fq1", fullName = "input_fq_file1", required = true, doc = "Input Fastq file to extract reads from (single-end fastq or, if paired, first end of the pair fastq)")
+  var fastq: File = _
+
+  @Input(shortName = "fq2", fullName = "input_fq_file2", required = false, doc = "Input Fastq file to extract reads from (if paired, second end of the pair fastq).")
+  var secondEndFastQ: File = _
+
+  @Output(shortName = "bam", fullName = "output_bam_file", required = true, doc = "Output bam file .")
+  var bam: File = _
+
+  @Argument(shortName = "SM", fullName = "SM", required = false, doc = "SM")
+  var SM: String = "SM"
+
+  @Argument(shortName = "LIB", fullName = "LIB", required = false, doc = "LIB")
+  var LIB: String = "LIB"
+
+  @Argument(shortName = "PU", fullName = "PU", required = false, doc = "PU")
+  var PU: String = "PU"
+
+  @Argument(shortName = "RG", fullName = "RG", required = false, doc = "RG")
+  var RG: String = "RG"
+
+  @Argument(shortName = "PL", fullName = "PL", required = false, doc = "PL")
+  var PL: String = "illumina"
+
+  @Argument(shortName = "CN", fullName = "CN", required = false, doc = "CN")
+  var CN: String = "CN"
+
+
+//  override def inputBams = Seq(fastq)
+//  override def outputBam = bam
+//  this.sortOrder = null
+  val createIndex:Boolean = true
+  override def commandLine = super.commandLine +
+    required("FASTQ=" + fastq) +
+    optional("FASTQ2=", secondEndFastQ, spaceSeparated=false) +
+    required("OUTPUT=" + bam) +
+    optional("READ_GROUP_NAME=", RG, spaceSeparated=false) +
+    required("SAMPLE_NAME=" + SM) +
+    optional("LIBRARY_NAME=", LIB, spaceSeparated=false) +
+    optional("PLATFORM_UNIT=", PU, spaceSeparated=false) +
+    optional("PLATFORM=", PL, spaceSeparated=false) +
+    optional("CREATE_INDEX=", createIndex, spaceSeparated=false) +
+    optional("SEQUENCING_CENTER=", CN, spaceSeparated=false)
+}