From ab75933799b58cfcc4414fd1fd3b37b09364f871 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 13:32:18 +0200
Subject: [PATCH] Replace getChr for getContig
---
.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 4 ++--
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala | 4 ++--
.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala | 2 +-
7 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
index 2646ea961..6136c146b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
@@ -137,7 +137,7 @@ object AnnotateVcfWithBed extends ToolCommand {
logger.info("Start reading vcf records")
for (record <- reader) {
- val overlaps = bedRecords.getOrElse(record.getChr, Nil).filter(x => {
+ val overlaps = bedRecords.getOrElse(record.getContig, Nil).filter(x => {
record.getStart <= x._2 && record.getEnd >= x._1
})
if (overlaps.isEmpty) {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
index ba148881c..2797ffc2d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
@@ -97,7 +97,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
val countReports: Map[String, CountReport] = bamReaders.map(x => (x._1, new CountReport))
val refAllele = vcfRecord.getReference.getBaseString
for ((sample, bamReader) <- bamReaders) {
- val queryInterval = new QueryInterval(bamHeaders(sample).getSequenceIndex(vcfRecord.getChr),
+ val queryInterval = new QueryInterval(bamHeaders(sample).getSequenceIndex(vcfRecord.getContig),
vcfRecord.getStart, vcfRecord.getStart + refAllele.length - 1)
val bamIter = bamReader.query(Array(queryInterval), false)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 892ce397d..8a5b05f6e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -131,7 +131,7 @@ object MergeAlleles extends ToolCommand {
}
val alleles: mutable.Set[Allele] = mutable.Set()
val builder = new VariantContextBuilder
- builder.chr(records.head.getChr)
+ builder.chr(records.head.getContig)
builder.start(records.head.getStart)
for (record <- records) {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index d34e8cf9d..47af91bf3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -542,7 +542,7 @@ object VcfStats extends ToolCommand {
else addToBuffer(tag, value, found = true)
}
- Map(record.getChr -> buffer.toMap, "total" -> buffer.toMap)
+ Map(record.getContig -> buffer.toMap, "total" -> buffer.toMap)
}
/** Function to check sample/genotype specific stats */
@@ -593,7 +593,7 @@ object VcfStats extends ToolCommand {
else addToBuffer(tag, value, found = true)
}
- Map(record.getChr -> buffer.toMap, "total" -> buffer.toMap)
+ Map(record.getContig -> buffer.toMap, "total" -> buffer.toMap)
}
/** Function to write 1 specific genotype field */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
index ab1f9d8cb..995efcdd2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
@@ -109,7 +109,7 @@ object VcfToTsv extends ToolCommand {
writer.println(sortedFields.mkString("#", commandArgs.separator, ""))
for (vcfRecord <- reader) {
val values: mutable.Map[String, Any] = mutable.Map()
- values += "CHROM" -> vcfRecord.getChr
+ values += "CHROM" -> vcfRecord.getContig
values += "POS" -> vcfRecord.getStart
values += "ID" -> vcfRecord.getID
values += "REF" -> vcfRecord.getReference.getBaseString
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 9009d2918..2415d89a2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -103,10 +103,10 @@ object VcfWithVcf extends ToolCommand {
var counter = 0
for (record <- reader) {
val secondaryRecords = if (commandArgs.matchAllele) {
- secondaryReader.query(record.getChr, record.getStart, record.getEnd).toList.
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
} else {
- secondaryReader.query(record.getChr, record.getStart, record.getEnd).toList
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
}
val fieldMap = (for (
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index f010c1cc7..96a9dc436 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -87,7 +87,7 @@ object WipeReads extends ToolCommand {
def makeIntervalFromBed(inFile: File): Iterator[Interval] =
asScalaIteratorConverter(getFeatureReader(inFile.toPath.toString, new BEDCodec(), false).iterator)
.asScala
- .map(x => new Interval(x.getChr, x.getStart, x.getEnd))
+ .map(x => new Interval(x.getContig, x.getStart, x.getEnd))
/**
* Parses a refFlat file to yield Interval objects
--
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