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biopet.biopet
Commits
6fa7f040
Commit
6fa7f040
authored
Dec 23, 2016
by
Peter van 't Hof
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Replace old files with 1 file
parent
299875bb
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29 additions
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41 deletions
+29
-41
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
...main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
+21
-9
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
+8
-32
No files found.
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
View file @
6fa7f040
...
...
@@ -87,28 +87,40 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
(
for
(
sample
<-
samples
)
yield
sample
->
{
keySet
.
map
(
key
=>
key
.
toString
->
this
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
chr
,
Map
[
String
,
Map
[
String
,
Int
]]()).
getOrElse
(
field
,
Map
[
String
,
Int
]()).
getOrElse
(
key
.
toString
,
0
)
).
toMap
key
.
toString
->
this
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
chr
,
Map
[
String
,
Map
[
Any
,
Int
]]()).
getOrElse
(
field
,
Map
[
Any
,
Int
]()).
get
(
key
)
).
filter
(
_
.
_2
.
isDefined
).
toMap
}).
toMap
}
/** This will generate stats for one contig */
def
getContigStats
(
contig
:
String
,
samples
:
List
[
String
],
genotypeFields
:
List
[
String
],
infoFields
:
List
[
String
])
:
Map
[
String
,
Any
]
=
{
def
getContigStats
(
contig
:
String
,
samples
:
List
[
String
],
genotypeFields
:
List
[
String
]
=
Nil
,
infoFields
:
List
[
String
]
=
Nil
,
sampleDistributions
:
List
[
String
]
=
Nil
)
:
Map
[
String
,
Any
]
=
{
Map
(
"genotype"
->
genotypeFields
.
map
(
f
=>
f
->
getGenotypeField
(
samples
,
f
,
contig
)).
toMap
,
"info"
->
infoFields
.
map
(
f
=>
f
->
getField
(
f
,
contig
))
"info"
->
infoFields
.
map
(
f
=>
f
->
getField
(
f
,
contig
)).
toMap
,
"sample_distributions"
->
sampleDistributions
.
map
(
f
=>
f
->
getField
(
"SampleDistribution-"
+
f
,
contig
)).
toMap
)
}
/** This will generate stats for total */
def
getTotalStats
(
samples
:
List
[
String
],
genotypeFields
:
List
[
String
],
infoFields
:
List
[
String
])
=
getContigStats
(
"total"
,
samples
,
genotypeFields
,
infoFields
)
def
getTotalStats
(
samples
:
List
[
String
],
genotypeFields
:
List
[
String
]
=
Nil
,
infoFields
:
List
[
String
]
=
Nil
,
sampleDistributions
:
List
[
String
]
=
Nil
)
=
getContigStats
(
"total"
,
samples
,
genotypeFields
,
infoFields
,
sampleDistributions
)
/** This will generate stats for total and contigs separated */
def
getAllStats
(
contigs
:
List
[
String
],
samples
:
List
[
String
],
genotypeFields
:
List
[
String
],
infoFields
:
List
[
String
])
:
Map
[
String
,
Any
]
=
{
def
getAllStats
(
contigs
:
List
[
String
],
samples
:
List
[
String
],
genotypeFields
:
List
[
String
]
=
Nil
,
infoFields
:
List
[
String
]
=
Nil
,
sampleDistributions
:
List
[
String
]
=
Nil
)
:
Map
[
String
,
Any
]
=
{
Map
(
"contigs"
->
contigs
.
map
(
c
=>
c
->
getContigStats
(
c
,
samples
,
genotypeFields
,
infoFields
)).
toMap
,
"total"
->
getTotalStats
(
samples
,
genotypeFields
,
infoFields
)
"contigs"
->
contigs
.
map
(
c
=>
c
->
getContigStats
(
c
,
samples
,
genotypeFields
,
infoFields
,
sampleDistributions
)).
toMap
,
"total"
->
getTotalStats
(
samples
,
genotypeFields
,
infoFields
,
sampleDistributions
)
)
}
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @
6fa7f040
...
...
@@ -20,14 +20,13 @@ import htsjdk.samtools.util.Interval
import
htsjdk.variant.variantcontext.
{
Genotype
,
VariantContext
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
nl.lumc.sasc.biopet.utils.
{
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
import
scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.Random
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration._
import
scala.concurrent.
{
Await
,
Future
}
...
...
@@ -248,33 +247,10 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"Done reading vcf records"
)
// Writing info fields to tsv files
val
infoOutputDir
=
new
File
(
cmdArgs
.
outputDir
,
"infotags"
)
stats
.
writeField
(
"general"
,
cmdArgs
.
outputDir
)
for
(
field
<-
adInfoTags
.
distinct
.
par
)
{
stats
.
writeField
(
field
,
infoOutputDir
)
for
(
line
<-
FastaUtils
.
getCachedDict
(
cmdArgs
.
referenceFile
).
getSequences
)
{
val
chr
=
line
.
getSequenceName
stats
.
writeField
(
field
,
new
File
(
infoOutputDir
,
"chrs"
+
File
.
separator
+
chr
),
chr
=
chr
)
}
}
// Write genotype field to tsv files
val
genotypeOutputDir
=
new
File
(
cmdArgs
.
outputDir
,
"genotypetags"
)
stats
.
writeGenotypeField
(
samples
,
"general"
,
cmdArgs
.
outputDir
,
prefix
=
"genotype"
)
for
(
field
<-
adGenotypeTags
.
distinct
.
par
)
{
stats
.
writeGenotypeField
(
samples
,
field
,
genotypeOutputDir
)
for
(
line
<-
FastaUtils
.
getCachedDict
(
cmdArgs
.
referenceFile
).
getSequences
)
{
val
chr
=
line
.
getSequenceName
stats
.
writeGenotypeField
(
samples
,
field
,
new
File
(
genotypeOutputDir
,
"chrs"
+
File
.
separator
+
chr
),
chr
=
chr
)
}
}
// Write sample distributions to tsv files
val
sampleDistributionsOutputDir
=
new
File
(
cmdArgs
.
outputDir
,
"sample_distributions"
)
for
(
field
<-
sampleDistributions
)
{
stats
.
writeField
(
"SampleDistribution-"
+
field
,
sampleDistributionsOutputDir
)
}
val
allWriter
=
new
PrintWriter
(
new
File
(
cmdArgs
.
outputDir
,
"all.json"
))
val
json
=
ConfigUtils
.
mapToJson
(
stats
.
getAllStats
(
FastaUtils
.
getCachedDict
(
cmdArgs
.
referenceFile
).
getSequences
.
map
(
_
.
getSequenceName
).
toList
,
samples
,
adGenotypeTags
,
adInfoTags
,
sampleDistributions
))
allWriter
.
println
(
json
.
spaces2
)
allWriter
.
close
()
// Write general wiggle tracks
for
(
field
<-
cmdArgs
.
generalWiggle
)
{
...
...
@@ -379,7 +355,7 @@ object VcfStats extends ToolCommand {
val
skipTags
=
List
(
"QUAL"
,
"general"
)
for
(
tag
<-
additionalTags
if
!
skipTags
.
contains
(
tag
))
{
addToBuffer
(
tag
,
0
,
found
=
false
)
addToBuffer
(
tag
,
"not set"
,
found
=
false
)
}
Map
(
"total"
->
buffer
.
toMap
)
...
...
@@ -395,7 +371,7 @@ object VcfStats extends ToolCommand {
else
buffer
+=
key
->
(
map
+
(
value
->
map
.
getOrElse
(
value
,
0
)))
}
buffer
+=
"QUAL"
->
Map
(
Math
.
round
(
record
.
getPhredScaledQual
)
->
1
)
addToBuffer
(
"QUAL"
,
Math
.
round
(
record
.
getPhredScaledQual
),
true
)
addToBuffer
(
"SampleDistribution-Het"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHet
),
found
=
true
)
addToBuffer
(
"SampleDistribution-HetNonRef"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHetNonRef
),
found
=
true
)
...
...
@@ -410,7 +386,7 @@ object VcfStats extends ToolCommand {
addToBuffer
(
"SampleDistribution-Filtered"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isFiltered
),
found
=
true
)
addToBuffer
(
"SampleDistribution-Variant"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHetNonRef
||
genotype
.
isHet
||
genotype
.
isHomVar
),
found
=
true
)
addToBuffer
(
"general"
,
"Total"
,
found
=
true
)
addToBuffer
(
"general"
,
"Total"
,
true
)
addToBuffer
(
"general"
,
"Biallelic"
,
record
.
isBiallelic
)
addToBuffer
(
"general"
,
"ComplexIndel"
,
record
.
isComplexIndel
)
addToBuffer
(
"general"
,
"Filtered"
,
record
.
isFiltered
)
...
...
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