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biopet.biopet
Commits
da908cbb
Commit
da908cbb
authored
Nov 03, 2014
by
Peter van 't Hof
Browse files
Changed to SamReaderFactory
parent
ef085f81
Changes
5
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
da908cbb
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
htsjdk.samtools.S
AMFileReader
import
htsjdk.samtools.S
amReaderFactory
import
scala.collection.JavaConversions._
import
java.io.File
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
CombineGVCFs
}
...
...
@@ -185,7 +185,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
libraryOutput
.
mappedBamFile
=
mapping
.
outputFiles
(
"finalBamFile"
)
}
else
{
var
readGroupOke
=
true
val
inputSam
=
new
SAMFileReader
(
bamFile
)
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
bamFile
)
val
header
=
inputSam
.
getFileHeader
.
getReadGroups
for
(
readGroup
<-
inputSam
.
getFileHeader
.
getReadGroups
)
{
if
(
readGroup
.
getSample
!=
sampleID
)
logger
.
warn
(
"Sample ID readgroup in bam file is not the same"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
da908cbb
package
nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMSequenceRecord
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
...
...
@@ -68,7 +67,7 @@ object BedToInterval extends ToolCommand {
val
writer
=
new
PrintWriter
(
commandArgs
.
outputFile
)
val
inputSam
=
new
SAMFileReader
(
commandArgs
.
bamFile
)
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
commandArgs
.
bamFile
)
val
refs
=
for
(
SQ
<-
inputSam
.
getFileHeader
.
getSequenceDictionary
.
getSequences
.
toArray
)
yield
{
val
record
=
SQ
.
asInstanceOf
[
SAMSequenceRecord
]
writer
.
write
(
"@SQ\tSN:"
+
record
.
getSequenceName
+
"\tLN:"
+
record
.
getSequenceLength
+
"\n"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
da908cbb
package
nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMRecord
import
htsjdk.samtools.
{
SAMRecord
,
SamReaderFactory
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
...
...
@@ -57,7 +56,7 @@ object BiopetFlagstat extends ToolCommand {
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
inputSam
=
new
SAMFileReader
(
commandArgs
.
inputFile
)
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
commandArgs
.
inputFile
)
val
iterSam
=
if
(
commandArgs
.
region
==
None
)
inputSam
.
iterator
else
{
val
regionRegex
=
"""(.*):(.*)-(.*)"""
.
r
commandArgs
.
region
.
get
match
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
View file @
da908cbb
package
nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.QueryInterval
import
htsjdk.samtools.SAMRecord
import
htsjdk.samtools.
{
QueryInterval
,
SamReaderFactory
,
SAMRecord
,
SamReader
}
import
htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.variantcontext.VariantContextBuilder
import
htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
...
...
@@ -69,7 +67,8 @@ object CheckAllelesVcfInBam extends ToolCommand {
if
(
commandArgs
.
bamFiles
.
size
!=
commandArgs
.
samples
.
size
)
logger
.
warn
(
"Number of samples is diffrent then number of bam files, left over will be removed"
)
val
bamReaders
:
Map
[
String
,
SAMFileReader
]
=
Map
(
commandArgs
.
samples
zip
commandArgs
.
bamFiles
.
map
(
x
=>
new
SAMFileReader
(
x
))
:
_
*
)
val
samReaderFactory
=
SamReaderFactory
.
makeDefault
val
bamReaders
:
Map
[
String
,
SamReader
]
=
Map
(
commandArgs
.
samples
zip
commandArgs
.
bamFiles
.
map
(
x
=>
samReaderFactory
.
open
(
x
))
:
_
*
)
val
bamHeaders
=
bamReaders
.
map
(
x
=>
(
x
.
_1
,
x
.
_2
.
getFileHeader
))
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputFile
,
false
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
View file @
da908cbb
/*
* Copyright 2014 pjvan_thof.
*
* Licensed 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
nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.QueryInterval
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.ValidationStringency
import
htsjdk.samtools.SAMRecord
import
htsjdk.samtools.
{
QueryInterval
,
SAMRecord
,
SamReaderFactory
,
ValidationStringency
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommand
import
scala.io.Source
...
...
@@ -44,8 +25,9 @@ object FindRepeatsPacBio extends ToolCommand {
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
bamReader
=
new
SAMFileReader
(
commandArgs
.
inputBam
)
bamReader
.
setValidationStringency
(
ValidationStringency
.
SILENT
)
val
bamReader
=
SamReaderFactory
.
makeDefault
.
validationStringency
(
ValidationStringency
.
SILENT
)
.
open
(
commandArgs
.
inputBam
)
val
bamHeader
=
bamReader
.
getFileHeader
val
header
=
List
(
"chr"
,
"startPos"
,
"stopPos"
,
"Repeat_seq"
,
"repeatLength"
,
...
...
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