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biopet.biopet
Commits
a79f7d0f
Commit
a79f7d0f
authored
Mar 19, 2015
by
Peter van 't Hof
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Added sample distributions
parent
2a838ba2
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+26
-0
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
a79f7d0f
...
...
@@ -247,6 +247,9 @@ object VcfStats extends ToolCommand {
val
defaultInfoFields
=
List
(
"QUAL"
,
"general"
,
"AC"
,
"AF"
,
"AN"
,
"DP"
)
val
sampleDistributions
=
List
(
"Het"
,
"HetNonRef"
,
"Hom"
,
"HomRef"
,
"HomVar"
,
"Mixed"
,
"NoCall"
,
"NonInformative"
,
"Available"
,
"Called"
,
"Filtered"
,
"Variant"
)
/**
* @param args the command line arguments
*/
...
...
@@ -373,6 +376,7 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"Done reading vcf records"
)
// Writing info fields to tsv files
val
infoOutputDir
=
new
File
(
commandArgs
.
outputDir
,
"infotags"
)
writeField
(
stats
,
"general"
,
commandArgs
.
outputDir
)
for
(
field
<-
(
adInfoTags
).
distinct
.
par
)
{
...
...
@@ -383,6 +387,7 @@ object VcfStats extends ToolCommand {
}
}
// Write genotype field to tsv files
val
genotypeOutputDir
=
new
File
(
commandArgs
.
outputDir
,
"genotypetags"
)
writeGenotypeField
(
stats
,
samples
,
"general"
,
commandArgs
.
outputDir
,
prefix
=
"genotype"
)
for
(
field
<-
(
adGenotypeTags
).
distinct
.
par
)
{
...
...
@@ -393,11 +398,19 @@ object VcfStats extends ToolCommand {
}
}
// Write sample distributions to tsv files
val
sampleDistributionsOutputDir
=
new
File
(
commandArgs
.
outputDir
,
"sample_distributions"
)
for
(
field
<-
sampleDistributions
)
{
writeField
(
stats
,
"SampleDistribution-"
+
field
,
sampleDistributionsOutputDir
)
}
// Write general wiggle tracks
for
(
field
<-
commandArgs
.
generalWiggle
)
{
val
file
=
new
File
(
commandArgs
.
outputDir
,
"wigs"
+
File
.
separator
+
"general-"
+
field
+
".wig"
)
writeWiggle
(
intervals
,
field
,
"count"
,
file
,
false
)
}
// Write sample wiggle tracks
for
(
field
<-
commandArgs
.
genotypeWiggle
;
sample
<-
samples
)
{
val
file
=
new
File
(
commandArgs
.
outputDir
,
"wigs"
+
File
.
separator
+
"genotype-"
+
sample
+
"-"
+
field
+
".wig"
)
writeWiggle
(
intervals
,
field
,
sample
,
file
,
true
)
...
...
@@ -471,6 +484,19 @@ object VcfStats extends ToolCommand {
buffer
+=
"QUAL"
->
Map
(
record
.
getPhredScaledQual
->
1
)
addToBuffer
(
"SampleDistribution-Het"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHet
),
true
)
addToBuffer
(
"SampleDistribution-HetNonRef"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHetNonRef
),
true
)
addToBuffer
(
"SampleDistribution-Hom"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHom
),
true
)
addToBuffer
(
"SampleDistribution-HomRef"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHomRef
),
true
)
addToBuffer
(
"SampleDistribution-HomVar"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHomVar
),
true
)
addToBuffer
(
"SampleDistribution-Mixed"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isMixed
),
true
)
addToBuffer
(
"SampleDistribution-NoCall"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isNoCall
),
true
)
addToBuffer
(
"SampleDistribution-NonInformative"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isNonInformative
),
true
)
addToBuffer
(
"SampleDistribution-Available"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isAvailable
),
true
)
addToBuffer
(
"SampleDistribution-Called"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isCalled
),
true
)
addToBuffer
(
"SampleDistribution-Filtered"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isFiltered
),
true
)
addToBuffer
(
"SampleDistribution-Variant"
,
record
.
getGenotypes
.
count
(
genotype
=>
genotype
.
isHetNonRef
||
genotype
.
isHet
||
genotype
.
isHomVar
),
true
)
addToBuffer
(
"general"
,
"Total"
,
true
)
addToBuffer
(
"general"
,
"Biallelic"
,
record
.
isBiallelic
)
addToBuffer
(
"general"
,
"ComplexIndel"
,
record
.
isComplexIndel
)
...
...
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