{"action":"created","comment":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/comments/58309099","id":58309099,"diff_hunk":"@@ -0,0 +1,143 @@\n+/*\n+ * The MIT License\n+ *\n+ * Copyright (c) 2016 Fulcrum Genomics LLC\n+ *\n+ * Permission is hereby granted, free of charge, to any person obtaining a copy\n+ * of this software and associated documentation files (the \"Software\"), to deal\n+ * in the Software without restriction, including without limitation the rights\n+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n+ * copies of the Software, and to permit persons to whom the Software is\n+ * furnished to do so, subject to the following conditions:\n+ *\n+ * The above copyright notice and this permission notice shall be included in\n+ * all copies or substantial portions of the Software.\n+ *\n+ * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n+ * THE SOFTWARE.\n+ */\n+\n+package com.fulcrumgenomics.util\n+\n+import com.fulcrumgenomics.util.BaseSymbol._\n+import com.fulcrumgenomics.util.ReadSegment._\n+\n+object ReadStructure {\n+  private val segmentPattern = s\"\\\\d+[${SymbolChars.mkString}]\".r\n+  private val readStructurePattern = s\"(\\\\d+[${SymbolChars.mkString}])+\".r\n+\n+  /** Creates a read structure from a string */\n+  def apply(readStructure: String): ReadStructure = {\n+    if (readStructurePattern.findAllIn(readStructure).mkString.length != readStructure.length) {\n+      throw new IllegalArgumentException(\"Read structure was not valid: \" + readStructure)\n+    }\n+    val segments = segmentPattern.findAllIn(readStructure).toSeq\n+    val lengths = segments.map(seg => Integer.parseInt(seg.substring(0, seg.length-1)))\n+    new ReadStructure(segs = segments.zipWithIndex.map {\n+      case (seg, idx) =>\n+        val offset = lengths.slice(0, idx).sum\n+        val length = lengths(idx)\n+        if (length == 0) throw new IllegalArgumentException(\"Read structure had a segment with zero length: \" + seg)\n+        seg.substring(seg.length-1).head match {\n+          case TemplateSymbol.symbol         => new Template(offset=offset, length=length)\n+          case SampleBarcodeSymbol.symbol    => new SampleBarcode(offset=offset, length=length)\n+          case MolecularBarcodeSymbol.symbol => new MolecularBarcode(offset=offset, length=length)\n+          case SkipSymbol.symbol             => new Skip(offset=offset, length=length)\n+          case s                             => throw new IllegalArgumentException(\"Read segment type unknown: \" + s)\n+        }\n+    }.toTraversable)\n+  }\n+\n+  /** Splits the given bases into tuples with its associated read segment. */\n+  def extract(bases: String, readStructure: ReadStructure, symbol: Option[BaseSymbol] = None, strict: Boolean = true): Seq[(String, ReadSegment)] = {\n+    readStructure.filter(s => s.symbol == symbol.getOrElse(s.symbol) && (strict || s.offset < bases.length)).map {\n+      segment =>\n+        val end = segment.offset + segment.length\n+        if (bases.length < end) {\n+          if (strict) throw new IllegalStateException(\"Not enough bases for read structure: \" + readStructure)\n+          else (bases.substring(segment.offset), ReadSegment(segment, bases.length-segment.offset))\n+        }\n+        else (bases.substring(segment.offset, end), segment)\n+    }\n+  }\n+\n+  /** Splits the given bases and qualities into triples with its associated read segment. */\n+  def extractWithQualities(bases: String, qualities: String, readStructure: ReadStructure, symbol: Option[BaseSymbol] = None, strict: Boolean = true): Seq[(String, String, ReadSegment)] = {\n+    assert(bases.length == qualities.length)\n+    readStructure.filter(s => s.symbol == symbol.getOrElse(s.symbol) && (strict || s.offset < bases.length)).map {\n+      segment =>\n+        val end = segment.offset + segment.length\n+        if (strict) {\n+          if (bases.length < end) throw new IllegalStateException(\"Not enough bases for read structure: \" + readStructure)\n+          if (qualities.length < end) throw new IllegalStateException(\"Not enough qualities for read structure: \" + readStructure)\n+        }\n+        if (bases.length < end) (bases.substring(segment.offset), qualities.substring(segment.offset), ReadSegment(segment, bases.length-segment.offset))\n+        else (bases.substring(segment.offset, end), qualities.substring(segment.offset, end), segment)\n+    }\n+  }\n+\n+  def template(rs: ReadStructure): Seq[Template] = rs.filter(_.symbol == TemplateSymbol).map(_.asInstanceOf[Template])\n+  def sampleBarcode(rs: ReadStructure): Seq[SampleBarcode] = rs.filter(_.symbol == SampleBarcodeSymbol).map(_.asInstanceOf[SampleBarcode])\n+  def molecularBarcode(rs: ReadStructure): Seq[MolecularBarcode] = rs.filter(_.symbol == MolecularBarcodeSymbol).map(_.asInstanceOf[MolecularBarcode])\n+  def skip(rs: ReadStructure): Seq[Skip] = rs.filter(_.symbol == SkipSymbol).map(_.asInstanceOf[Skip])\n+}\n+\n+/**\n+  * Describes the structure of a give read.  A read contains one or more read segments. A read segment describes\n+  * a contiguous stretch of bases of the same type (ex. template bases) of some length and some offset from the start\n+  * of the read.\n+  */\n+class ReadStructure private(segs: Traversable[ReadSegment]) extends scala.collection.immutable.Seq[ReadSegment] {\n+  private val segments: Seq[ReadSegment] = segs.toSeq\n+  def length: Int = segments.length\n+  def apply(idx: Int): ReadSegment = segments(idx)\n+  def iterator: Iterator[ReadSegment] = segments.iterator\n+  override def toString: String = segments.map(_.toString).mkString\n+  def totalBases: Int = segments.map(_.length).sum\n+}\n+\n+object BaseSymbol {\n+  sealed trait BaseSymbol {\n+    def symbol: Char\n+    override def toString: String = s\"$symbol\"\n+  }\n+  case object TemplateSymbol         extends BaseSymbol { override val symbol: Char = 'T' }\n+  case object SampleBarcodeSymbol    extends BaseSymbol { override val symbol: Char = 'B' }\n+  case object MolecularBarcodeSymbol extends BaseSymbol { override val symbol: Char = 'M' }\n+  case object SkipSymbol             extends BaseSymbol { override val symbol: Char = 'S' }\n+  val Symbols = Seq(TemplateSymbol, SampleBarcodeSymbol, MolecularBarcodeSymbol, SkipSymbol)\n+  val SymbolChars = Seq(TemplateSymbol, SampleBarcodeSymbol, MolecularBarcodeSymbol, SkipSymbol).map(_.symbol)\n+}","path":"src/main/scala/com/fulcrumgenomics/util/ReadStructure.scala","position":115,"original_position":115,"commit_id":"13a68d9dc183b91e8fcb2cbb6a29dcfbe60a2b43","original_commit_id":"13a68d9dc183b91e8fcb2cbb6a29dcfbe60a2b43","user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"body":"Might be nice to provide `def apply(s: String): SegmentType` and `def apply(ch: Char): SegmentType` method to resolve the segment types from symbols without having to write `match` statements in client code.","created_at":"2016-04-03T12:01:46Z","updated_at":"2016-04-03T12:01:46Z","html_url":"https://github.com/fulcrumgenomics/fgbio/pull/14#discussion_r58309099","pull_request_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/14","_links":{"self":{"href":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/comments/58309099"},"html":{"href":"https://github.com/fulcrumgenomics/fgbio/pull/14#discussion_r58309099"},"pull_request":{"href":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/14"}}},"pull_request":{"url":"https://api.github.com/repos/fulcrumgenomics/fgbio/pulls/14","id":64199519,"html_url":"https://github.com/fulcrumgenomics/fgbio/pull/14","diff_url":"https://github.com/fulcrumgenomics/fgbio/pull/14.diff","patch_url":"https://github.com/fulcrumgenomics/fgbio/pull/14.patch","issue_url":"https://api.github.com/repos/fulcrumgenomics/fgbio/issues/14","number":14,"state":"open","locked":false,"title":"Add a tool to annotate reads with their molecular 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