From eb8aef9357f1cd2c7e3b8c45af1d20ba98897786 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 18 Feb 2015 11:47:34 +0100
Subject: [PATCH] Fix picard summaries
---
.../pipelines/bammetrics/BamMetrics.scala | 1 +
.../CollectAlignmentSummaryMetrics.scala | 14 +-
.../picard/CollectInsertSizeMetrics.scala | 2 +-
.../test/resources/picard.alignmentMetrics | 12 +
.../test/resources/picard.insertsizemetrics | 717 ++++++++++++++++++
.../CollectAlignmentSummaryMetricsTest.scala | 23 +
.../picard/CollectInsertSizeMetricsTest.scala | 23 +
7 files changed, 786 insertions(+), 6 deletions(-)
create mode 100644 public/biopet-framework/src/test/resources/picard.alignmentMetrics
create mode 100644 public/biopet-framework/src/test/resources/picard.insertsizemetrics
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 506e42337..cbbf91da7 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -83,6 +83,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
for (bedFile <- bedFiles) {
+ //TODO: Add target jobs to summary
val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
add(targetInterval, true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 8fad20529..f69114521 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -66,11 +66,15 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
def summaryData: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
- (for (category <- 0 to content.size) yield {
- content(category)(0) -> (for (i <- 1 to header.size) yield {
- header(i).toLowerCase -> content(category)(i)
- }).toMap
- }).toMap
+ (for (category <- 0 until content.size) yield {
+ content(category)(0) -> (
+ for (
+ i <- 1 until header.size if i < content(category).size
+ ) yield {
+ header(i).toLowerCase -> content(category)(i)
+ }).toMap
+ }
+ ).toMap
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index f83298822..9585491f9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -75,7 +75,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
def summaryData: Map[String, Any] = {
val (header, content) = Picard.getMetrics(output)
- (for (i <- 0 to header.size)
+ (for (i <- 0 to header.size if i < content.head.size)
yield (header(i).toLowerCase -> content.head(i))).toMap
}
}
diff --git a/public/biopet-framework/src/test/resources/picard.alignmentMetrics b/public/biopet-framework/src/test/resources/picard.alignmentMetrics
new file mode 100644
index 000000000..2f05f08c4
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/picard.alignmentMetrics
@@ -0,0 +1,12 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectAlignmentSummaryMetrics INPUT=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_2/8080_2#43-8080_2.dedup.bam OUTPUT=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_2/metrics/8080_2#43-8080_2.dedup.alignmentMetrics REFERENCE_SEQUENCE=/home/cwknetsch/pipeline_pilot/input/reference/M120_23032012.fasta ASSUME_SORTED=true TMP_DIR=[/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/.queue/tmp] CREATE_INDEX=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Tue Feb 17 15:40:01 CET 2015
+
+## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
+CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
+FIRST_OF_PAIR 664252 664252 1 0 606507 0.913068 60008919 594828 58868522 58661158 0 0.000976 0.000962 0.00003 99.071709 603803 0.995542 0 0.499488 0.027347 0.000056
+SECOND_OF_PAIR 664252 664252 1 0 606337 0.912812 60044312 594744 58913706 58680340 0 0.000842 0.00083 0.000034 99.128317 603803 0.995821 0 0.500456 0.027347 0.000033
+PAIR 1328504 1328504 1 0 1212844 0.91294 120053231 1189572 117782228 117341498 0 0.000909 0.000896 0.000032 99.100013 1207606 0.995681 0 0.499972 0.027347 0.000044
+
+
diff --git a/public/biopet-framework/src/test/resources/picard.insertsizemetrics b/public/biopet-framework/src/test/resources/picard.insertsizemetrics
new file mode 100644
index 000000000..ae5131591
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/picard.insertsizemetrics
@@ -0,0 +1,717 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_2/metrics/8080_2#43-8080_2.dedup.insertsizemetrics.pdf INPUT=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_2/8080_2#43-8080_2.dedup.bam OUTPUT=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_2/metrics/8080_2#43-8080_2.dedup.insertsizemetrics REFERENCE_SEQUENCE=/home/cwknetsch/pipeline_pilot/input/reference/M120_23032012.fasta ASSUME_SORTED=true TMP_DIR=[/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/.queue/tmp] CREATE_INDEX=true DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Tue Feb 17 15:40:01 CET 2015
+
+## METRICS CLASS picard.analysis.InsertSizeMetrics
+MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
+249 50 19 4010275 269.721498 88.166884 585513 FR 21 41 59 81 101 123 151 191 297 849
+
+## HISTOGRAM java.lang.Integer
+insert_size All_Reads.fr_count
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diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
new file mode 100644
index 000000000..51139812f
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
@@ -0,0 +1,23 @@
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvan_thof on 2/18/15.
+ */
+class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
+
+ @Test
+ def summaryData: Unit = {
+ val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
+ val job = new CollectAlignmentSummaryMetrics(null)
+ job.output = file
+
+ job.summaryData
+ }
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
new file mode 100644
index 000000000..fc0c563e8
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
@@ -0,0 +1,23 @@
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvan_thof on 2/18/15.
+ */
+class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
+
+ @Test
+ def summaryData: Unit = {
+ val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
+ val job = new CollectInsertSizeMetrics(null)
+ job.output = file
+
+ job.summaryData
+ }
+}
--
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