-
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.
Merge pull request #568 from nfergu/timersfix
Moved the Timers object from bdg-utils back to ADAM
- Loading branch information
Showing
15 changed files
with
90 additions
and
14 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
76 changes: 76 additions & 0 deletions
76
adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/Timers.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 +1,76 @@ | ||
| /** | ||
| * 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.instrumentation | ||
|
|
||
| import org.bdgenomics.utils.instrumentation.Metrics | ||
|
|
||
| /** | ||
| * Contains [[Timers]] that are used to instrument ADAM. | ||
| */ | ||
| object Timers extends Metrics { | ||
|
|
||
| // File Loading | ||
| val LoadAlignmentRecords = timer("Load Alignment Records") | ||
| val BAMLoad = timer("BAM File Load") | ||
| val ParquetLoad = timer("Parquet File Load") | ||
|
|
||
| // Trim Reads | ||
| val TrimReadsInDriver = timer("Trim Reads") | ||
| val TrimRead = timer("Trim Reads") | ||
| val TrimCigar = timer("Trim Cigar") | ||
| val TrimMDTag = timer("Trim MD Tag") | ||
|
|
||
| // Trim Low Quality Read Groups | ||
| val TrimLowQualityInDriver = timer("Trim Low Quality Read Groups") | ||
|
|
||
| // Mark Duplicates | ||
| val MarkDuplicatesInDriver = timer("Mark Duplicates") | ||
| val CreateReferencePositionPair = timer("Create Reference Position Pair") | ||
| val PerformDuplicateMarking = timer("Perform Duplicate Marking") | ||
| val ScoreAndMarkReads = timer("Score and Mark Reads") | ||
| val MarkReads = timer("Mark Reads") | ||
|
|
||
| // Recalibrate Base Qualities | ||
| val BQSRInDriver = timer("Base Quality Recalibration") | ||
| val CreateKnownSnpsTable = timer("Create Known SNPs Table") | ||
| val RecalibrateRead = timer("Recalibrate Read") | ||
|
|
||
| // Realign Indels | ||
| val RealignIndelsInDriver = timer("Realign Indels") | ||
| val FindTargets = timer("Find Targets") | ||
| val CreateIndelRealignmentTargets = timer("Create Indel Realignment Targets for Read") | ||
| val SortTargets = timer("Sort Targets") | ||
| val JoinTargets = timer("Join Targets") | ||
| val MapTargets = timer("Map Targets") | ||
| val RealignTargetGroup = timer("Realign Target Group") | ||
| val GetReferenceFromReads = timer("Get Reference From Reads") | ||
| val SweepReadOverReferenceForQuality = timer("Sweep Read Over Reference For Quality") | ||
|
|
||
| // Sort Reads | ||
| val SortReads = timer("Sort Reads") | ||
|
|
||
| // File Saving | ||
| val SAMSave = timer("SAM Save") | ||
| val ConvertToSAM = timer("Convert To SAM") | ||
| val ConvertToSAMRecord = timer("Convert To SAM Record") | ||
| val SaveAsADAM = timer("Save File In ADAM Format") | ||
| val WriteADAMRecord = timer("Write ADAM Record") | ||
| val WriteBAMRecord = timer("Write BAM Record") | ||
| val WriteSAMRecord = timer("Write SAM Record") | ||
|
|
||
| } |
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
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