-
Notifications
You must be signed in to change notification settings - Fork 308
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
24 changed files
with
658 additions
and
48 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
161 changes: 161 additions & 0 deletions
161
adam-core/src/main/java/org/bdgenomics/adam/io/BAMFilteredRecordReader.scala
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package org.bdgenomics.adam.io | ||
|
|
||
| import hbparquet.hadoop.util.ContextUtil | ||
| import htsjdk.samtools.BAMRecordCodec | ||
| import htsjdk.samtools.ValidationStringency | ||
| import htsjdk.samtools.SAMRecord | ||
| import htsjdk.samtools.util.BlockCompressedInputStream | ||
| import org.apache.hadoop.conf.Configuration | ||
| import org.apache.hadoop.fs.FileSystem | ||
| import org.apache.hadoop.fs.FSDataInputStream | ||
| import org.apache.hadoop.fs.Path | ||
| import org.apache.hadoop.io.LongWritable | ||
| import org.apache.hadoop.mapreduce.InputSplit | ||
| import org.apache.hadoop.mapreduce.RecordReader | ||
| import org.apache.hadoop.mapreduce.TaskAttemptContext | ||
| import org.bdgenomics.adam.models.ReferenceRegion | ||
| import org.seqdoop.hadoop_bam.util.SAMHeaderReader | ||
| import org.seqdoop.hadoop_bam.util.WrapSeekable | ||
| import org.seqdoop.hadoop_bam.SAMRecordWritable | ||
| import org.seqdoop.hadoop_bam.BAMRecordReader | ||
| import org.seqdoop.hadoop_bam.FileVirtualSplit | ||
| import org.seqdoop.hadoop_bam.BAMInputFormat | ||
| import scala.annotation.tailrec | ||
|
|
||
| object BAMFilteredRecordReader { | ||
| private var optViewRegion: Option[ReferenceRegion] = None | ||
|
|
||
| def setRegion(viewRegion: ReferenceRegion) { | ||
| optViewRegion = Some(viewRegion) | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Scala implementation of BAMRecordReader, but with | ||
| * nextKeyValue() that filters by ReferenceRegion | ||
| */ | ||
| class BAMFilteredRecordReader extends BAMRecordReader { | ||
|
|
||
| val key: LongWritable = new LongWritable() | ||
| val record: SAMRecordWritable = new SAMRecordWritable | ||
|
|
||
| var stringency: ValidationStringency = _ | ||
|
|
||
| var bci: BlockCompressedInputStream = _ | ||
| var codec: BAMRecordCodec = _ | ||
| var fileStart: Long = _ | ||
| var virtualEnd: Long = _ | ||
| var isInitialized: Boolean = false | ||
|
|
||
| override def initialize(spl: InputSplit, ctx: TaskAttemptContext) { | ||
| // Check to ensure this method is only be called once (see Hadoop API) | ||
| if (isInitialized) { | ||
| close() | ||
| } | ||
| isInitialized = true | ||
|
|
||
| val conf: Configuration = ContextUtil.getConfiguration(ctx) | ||
|
|
||
| val split: FileVirtualSplit = spl.asInstanceOf[FileVirtualSplit] | ||
| val file: Path = split.getPath() | ||
| val fs: FileSystem = file.getFileSystem(conf) | ||
|
|
||
| this.stringency = SAMHeaderReader.getValidationStringency(conf) | ||
|
|
||
| val in: FSDataInputStream = fs.open(file) | ||
|
|
||
| // Sets codec to translate between in-memory and disk representation of record | ||
| codec = new BAMRecordCodec(SAMHeaderReader.readSAMHeaderFrom(in, conf)) | ||
|
|
||
| in.seek(0) | ||
|
|
||
| bci = new BlockCompressedInputStream( | ||
| new WrapSeekable[FSDataInputStream]( | ||
| in, fs.getFileStatus(file).getLen(), file)) | ||
|
|
||
| // Gets BGZF virtual offset for the split | ||
| val virtualStart = split.getStartVirtualOffset() | ||
|
|
||
| fileStart = virtualStart >>> 16 | ||
| virtualEnd = split.getEndVirtualOffset() | ||
|
|
||
| // Starts looking from the BGZF virtual offset | ||
| bci.seek(virtualStart) | ||
| // Reads records from this input stream | ||
| codec.setInputStream(bci) | ||
| } | ||
|
|
||
| override def close() = { | ||
| bci.close() | ||
| } | ||
|
|
||
| override def getCurrentKey(): LongWritable = { | ||
| key | ||
| } | ||
|
|
||
| override def getCurrentValue(): SAMRecordWritable = { | ||
| record | ||
| } | ||
|
|
||
| /** | ||
| * This method gets the nextKeyValue for our RecordReader, but filters by only | ||
| * returning records within a specified ReferenceRegion. | ||
| * This function is tail recursive to avoid stack overflow when predicate data | ||
| * can be sparse. | ||
| */ | ||
| @tailrec final override def nextKeyValue(): Boolean = { | ||
| if (bci.getFilePointer() >= virtualEnd) { | ||
| false | ||
| } else { | ||
| val r: SAMRecord = codec.decode() | ||
|
|
||
| // Since we're reading from a BAMRecordCodec directly we have to set the | ||
| // validation stringency ourselves. | ||
| if (this.stringency != null) { | ||
| r.setValidationStringency(this.stringency) | ||
| } | ||
|
|
||
| // This if/else block pushes the predicate down onto a BGZIP block that | ||
| // the index has said contains data in our specified region. | ||
| if (r == null) { | ||
| false | ||
| } else { | ||
| val start = r.getStart | ||
| val end = r.getEnd | ||
| val refReg = BAMFilteredRecordReader.optViewRegion.get | ||
| val regStart = refReg.start | ||
| val regEnd = refReg.end | ||
|
|
||
| if ((r.getContig() == refReg.referenceName) && | ||
| (((start >= regStart) && (end <= regEnd)) | ||
| || ((start <= regStart) && (end >= regStart) && (end <= regEnd)) | ||
| || ((end >= regEnd) && (start >= regStart) && (start <= regEnd)))) { | ||
| key.set(BAMRecordReader.getKey(r)) | ||
| record.set(r) | ||
| true | ||
| } else { | ||
| nextKeyValue() | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| } |
102 changes: 102 additions & 0 deletions
102
adam-core/src/main/java/org/bdgenomics/adam/io/IndexedBamInputFormat.scala
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package htsjdk.samtools | ||
|
|
||
| import htsjdk.samtools.util.BlockCompressedFilePointerUtil | ||
| import java.io.File | ||
| import java.io.FileNotFoundException | ||
| import org.apache.hadoop.fs.{ FileSystem, Path } | ||
| import org.apache.hadoop.io.LongWritable | ||
| import org.apache.hadoop.mapreduce.JobContext | ||
| import org.apache.hadoop.mapreduce.RecordReader | ||
| import org.apache.hadoop.mapreduce.InputSplit | ||
| import org.apache.hadoop.mapreduce.TaskAttemptContext | ||
| import org.apache.hadoop.mapreduce.lib.input.FileSplit | ||
| import org.bdgenomics.adam.models.ReferenceRegion | ||
| import org.bdgenomics.adam.rdd.ADAMContext._ | ||
| import org.bdgenomics.adam.io.BAMFilteredRecordReader | ||
| import org.seqdoop.hadoop_bam.BAMInputFormat | ||
| import org.seqdoop.hadoop_bam.FileVirtualSplit | ||
| import org.seqdoop.hadoop_bam.SAMRecordWritable | ||
| import scala.collection.mutable | ||
|
|
||
| object IndexedBamInputFormat { | ||
|
|
||
| private var optFilePath: Option[Path] = None | ||
| private var optIndexFilePath: Option[Path] = None | ||
| private var optViewRegion: Option[ReferenceRegion] = None | ||
| private var optDict: Option[SAMSequenceDictionary] = None | ||
|
|
||
| def setVars(filePath: Path, indexFilePath: Path, viewRegion: ReferenceRegion, dict: SAMSequenceDictionary) { | ||
| optFilePath = Some(filePath) | ||
| optIndexFilePath = Some(indexFilePath) | ||
| optViewRegion = Some(viewRegion) | ||
| optDict = Some(dict) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| class IndexedBamInputFormat extends BAMInputFormat { | ||
|
|
||
| override def createRecordReader(split: InputSplit, ctx: TaskAttemptContext): RecordReader[LongWritable, SAMRecordWritable] = { | ||
| val rr: RecordReader[LongWritable, SAMRecordWritable] = new BAMFilteredRecordReader() | ||
| assert(IndexedBamInputFormat.optViewRegion.isDefined) | ||
| BAMFilteredRecordReader.setRegion(IndexedBamInputFormat.optViewRegion.get) | ||
| rr.initialize(split, ctx) | ||
| rr | ||
| } | ||
|
|
||
| override def getSplits(job: JobContext): java.util.List[InputSplit] = { | ||
| assert(IndexedBamInputFormat.optIndexFilePath.isDefined && | ||
| IndexedBamInputFormat.optFilePath.isDefined && | ||
| IndexedBamInputFormat.optViewRegion.isDefined && | ||
| IndexedBamInputFormat.optDict.isDefined) | ||
|
|
||
| val indexFilePath = IndexedBamInputFormat.optIndexFilePath.get | ||
|
|
||
| val idxFile: File = new File(indexFilePath.toString) | ||
| if (!idxFile.exists()) { | ||
| throw new java.io.FileNotFoundException("Bam index file not provided") | ||
| } else { | ||
| // Use index to get the chunks for a specific region, then use them to create InputSplits | ||
| val filePath = IndexedBamInputFormat.optFilePath.get | ||
| val viewRegion = IndexedBamInputFormat.optViewRegion.get | ||
| val refName = viewRegion.referenceName | ||
| val dict = IndexedBamInputFormat.optDict.get | ||
| val start = viewRegion.start.toInt | ||
| val end = viewRegion.end.toInt | ||
| val dbbfi: DiskBasedBAMFileIndex = new DiskBasedBAMFileIndex(idxFile, dict) | ||
| val referenceIndex: Int = dict.getSequenceIndex(refName) | ||
| // Get the chunks in the region we want (chunks give start and end file pointers into a BAM file) | ||
| var regions: List[Chunk] = dbbfi.getSpanOverlapping(referenceIndex, start, end).getChunks | ||
|
|
||
| var splits = new mutable.ListBuffer[FileVirtualSplit]() | ||
| for (chunk <- regions) { | ||
| // Create InputSplits from chunks in a given region | ||
| val start: Long = chunk.getChunkStart() | ||
| val end: Long = chunk.getChunkEnd() | ||
| val locs = Array[String]() | ||
| val newSplit = new FileVirtualSplit(filePath, start, end, locs) | ||
| splits += newSplit | ||
| } | ||
| splits.toList | ||
| } | ||
| } | ||
|
|
||
| } |
Oops, something went wrong.