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biopet.biopet
Commits
aa87e2ce
Commit
aa87e2ce
authored
Mar 03, 2015
by
Peter van 't Hof
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Added option to add all info and format fields
parent
9bca32a9
Changes
1
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103 additions
and
30 deletions
+103
-30
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+103
-30
No files found.
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
aa87e2ce
...
...
@@ -65,14 +65,20 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
object
VcfStats
extends
ToolCommand
{
/** Commandline argument */
case
class
Args
(
inputFile
:
File
=
null
,
outputDir
:
String
=
null
,
intervals
:
Option
[
File
]
=
None
)
extends
AbstractArgs
case
class
Args
(
inputFile
:
File
=
null
,
outputDir
:
File
=
null
,
intervals
:
Option
[
File
]
=
None
,
infoTags
:
List
[
String
]
=
Nil
,
genotypeTags
:
List
[
String
]
=
Nil
,
allInfoTags
:
Boolean
=
false
,
allGenotypeTags
:
Boolean
=
false
)
extends
AbstractArgs
/** Parsing commandline arguments */
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
opt
[
String
](
'o'
,
"outputDir"
)
required
()
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
opt
[
File
](
'o'
,
"outputDir"
)
required
()
unbounded
()
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputDir
=
x
)
}
//TODO: add interval argument
...
...
@@ -81,6 +87,18 @@ object VcfStats extends ToolCommand {
c.copy(intervals = Some(x))
}
*/
opt
[
String
](
"infoTag"
)
unbounded
()
valueName
(
"<tag>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
infoTags
=
x
::
c
.
infoTags
)
}
opt
[
String
](
"genotypeTag"
)
unbounded
()
valueName
(
"<tag>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
genotypeTags
=
x
::
c
.
genotypeTags
)
}
opt
[
Unit
](
"allInfoTags"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
allInfoTags
=
true
)
}
opt
[
Unit
](
"allGenotypeTags"
)
unbounded
()
action
{
(
x
,
c
)
=>
c
.
copy
(
allGenotypeTags
=
true
)
}
}
/**
...
...
@@ -165,6 +183,10 @@ object VcfStats extends ToolCommand {
protected
var
commandArgs
:
Args
=
_
val
defaultGenotypeFields
=
List
(
"DP"
,
"GQ"
,
"AD"
,
"AD-ref"
,
"AD-alt"
,
"AD-used"
,
"AD-not_used"
,
"general"
)
val
defaultInfoFields
=
List
(
"QUAL"
,
"general"
)
/**
* @param args the command line arguments
*/
...
...
@@ -177,6 +199,29 @@ object VcfStats extends ToolCommand {
val
header
=
reader
.
getFileHeader
val
samples
=
header
.
getSampleNamesInOrder
.
toList
val
adInfoTags
=
(
for
(
infoTag
<-
commandArgs
.
infoTags
if
!
defaultInfoFields
.
exists
(
_
==
infoTag
))
yield
{
require
(
header
.
getInfoHeaderLine
(
infoTag
)
!=
null
,
"Info tag '"
+
infoTag
+
"' not found in header of vcf file"
)
infoTag
})
:::
(
for
(
line
<-
header
.
getInfoHeaderLines
if
commandArgs
.
allInfoTags
if
!
defaultInfoFields
.
exists
(
_
==
line
.
getID
)
if
!
commandArgs
.
infoTags
.
exists
(
_
==
line
.
getID
))
yield
{
line
.
getID
}).
toList
val
adGenotypeTags
=
(
for
(
genotypeTag
<-
commandArgs
.
genotypeTags
if
!
defaultGenotypeFields
.
exists
(
_
==
genotypeTag
))
yield
{
require
(
header
.
getFormatHeaderLine
(
genotypeTag
)
!=
null
,
"Format tag '"
+
genotypeTag
+
"' not found in header of vcf file"
)
genotypeTag
})
:::
(
for
(
line
<-
header
.
getFormatHeaderLines
if
commandArgs
.
allGenotypeTags
if
!
defaultGenotypeFields
.
exists
(
_
==
line
.
getID
)
if
!
commandArgs
.
genotypeTags
.
exists
(
_
==
line
.
getID
)
if
line
.
getID
!=
"PL"
)
yield
{
line
.
getID
}).
toList
val
intervals
:
List
[
Interval
]
=
(
for
(
seq
<-
header
.
getSequenceDictionary
.
getSequences
;
...
...
@@ -227,10 +272,10 @@ object VcfStats extends ToolCommand {
for
(
record
<-
reader
.
query
(
interval
.
getSequence
,
interval
.
getStart
,
interval
.
getEnd
)
if
record
.
getStart
<=
interval
.
getEnd
)
{
mergeNestedStatsMap
(
stats
.
generalStats
,
checkGeneral
(
record
))
mergeNestedStatsMap
(
stats
.
generalStats
,
checkGeneral
(
record
,
adInfoTags
))
for
(
sample1
<-
samples
)
yield
{
val
genotype
=
record
.
getGenotype
(
sample1
)
mergeNestedStatsMap
(
stats
.
samplesStats
(
sample1
).
genotypeStats
,
checkGenotype
(
record
,
genotype
))
mergeNestedStatsMap
(
stats
.
samplesStats
(
sample1
).
genotypeStats
,
checkGenotype
(
record
,
genotype
,
adGenotypeTags
))
for
(
sample2
<-
samples
)
{
val
genotype2
=
record
.
getGenotype
(
sample2
)
if
(
genotype
.
getAlleles
==
genotype2
.
getAlleles
)
...
...
@@ -248,17 +293,35 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"Done reading vcf records"
)
writeField
(
"QUAL"
,
stats
.
generalStats
.
getOrElse
(
"total"
,
mutable
.
Map
()).
getOrElse
(
"QUAL"
,
mutable
.
Map
()))
writeField
(
"general"
,
stats
.
generalStats
.
getOrElse
(
"total"
,
mutable
.
Map
()).
getOrElse
(
"general"
,
mutable
.
Map
()))
writeGenotypeFields
(
stats
,
commandArgs
.
outputDir
+
"/genotype_"
,
samples
)
val
infoOutputDir
=
new
File
(
commandArgs
.
outputDir
,
"infotags"
)
writeField
(
stats
,
"general"
,
commandArgs
.
outputDir
)
for
(
field
<-
(
adInfoTags
:::
defaultInfoFields
).
distinct
.
par
)
{
writeField
(
stats
,
field
,
infoOutputDir
)
for
(
line
<-
header
.
getContigLines
)
{
val
chr
=
line
.
getSAMSequenceRecord
.
getSequenceName
writeField
(
stats
,
field
,
new
File
(
infoOutputDir
,
"chrs"
+
File
.
separator
+
chr
),
chr
=
chr
)
}
}
val
genotypeOutputDir
=
new
File
(
commandArgs
.
outputDir
,
"genotypetags"
)
writeGenotypeField
(
stats
,
samples
,
"general"
,
commandArgs
.
outputDir
,
prefix
=
"genotype"
)
for
(
field
<-
(
adGenotypeTags
:::
defaultGenotypeFields
).
distinct
.
par
)
{
writeGenotypeField
(
stats
,
samples
,
field
,
genotypeOutputDir
)
for
(
line
<-
header
.
getContigLines
)
{
val
chr
=
line
.
getSAMSequenceRecord
.
getSequenceName
writeGenotypeField
(
stats
,
samples
,
field
,
new
File
(
genotypeOutputDir
,
"chrs"
+
File
.
separator
+
chr
),
chr
=
chr
)
}
}
writeOverlap
(
stats
,
_
.
genotypeOverlap
,
commandArgs
.
outputDir
+
"/sample_compare/genotype_overlap"
,
samples
)
writeOverlap
(
stats
,
_
.
alleleOverlap
,
commandArgs
.
outputDir
+
"/sample_compare/allele_overlap"
,
samples
)
logger
.
info
(
"Done"
)
reader
.
close
()
}
/** Function to check all general stats, all info expect sample/genotype specific stats */
protected
def
checkGeneral
(
record
:
VariantContext
)
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
protected
def
checkGeneral
(
record
:
VariantContext
,
additionalTags
:
List
[
String
]
)
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
def
addToBuffer
(
key
:
String
,
value
:
Any
,
found
:
Boolean
)
:
Unit
=
{
...
...
@@ -289,11 +352,17 @@ object VcfStats extends ToolCommand {
addToBuffer
(
"general"
,
"SymbolicOrSV"
,
record
.
isSymbolicOrSV
)
addToBuffer
(
"general"
,
"Variant"
,
record
.
isVariant
)
for
(
tag
<-
additionalTags
)
{
val
value
=
record
.
getAttribute
(
tag
)
if
(
value
==
null
)
addToBuffer
(
tag
,
"notset"
,
true
)
else
addToBuffer
(
tag
,
value
,
true
)
}
Map
(
record
.
getChr
->
buffer
.
toMap
,
"total"
->
buffer
.
toMap
)
}
/** Function to check sample/genotype specific stats */
protected
def
checkGenotype
(
record
:
VariantContext
,
genotype
:
Genotype
)
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
protected
def
checkGenotype
(
record
:
VariantContext
,
genotype
:
Genotype
,
additionalTags
:
List
[
String
]
)
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
def
addToBuffer
(
key
:
String
,
value
:
Any
,
found
:
Boolean
)
:
Unit
=
{
...
...
@@ -332,29 +401,25 @@ object VcfStats extends ToolCommand {
}
}
Map
(
record
.
getChr
->
buffer
.
toMap
,
"total"
->
buffer
.
toMap
)
}
/** Function to write stats to tsv files */
protected
def
writeGenotypeFields
(
stats
:
Stats
,
prefix
:
String
,
samples
:
List
[
String
])
{
val
fields
=
List
(
"DP"
,
"GQ"
,
"AD"
,
"AD-ref"
,
"AD-alt"
,
"AD-used"
,
"AD-not_used"
,
"general"
)
for
(
field
<-
fields
)
{
writeGenotypeField
(
stats
,
prefix
,
samples
,
field
)
for
(
tag
<-
additionalTags
)
{
val
value
=
genotype
.
getAnyAttribute
(
tag
)
if
(
value
==
null
)
addToBuffer
(
tag
,
"notset"
,
true
)
else
addToBuffer
(
tag
,
value
,
true
)
}
}
protected
def
writeGenotypeField
(
stats
:
Stats
,
prefix
:
String
,
samples
:
List
[
String
],
field
:
String
)
:
Unit
=
{
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputFile
,
true
)
val
header
=
reader
.
getFileHeader
for
(
line
<-
header
.
getContigLines
)
{
writeGenotypeField
(
stats
,
prefix
,
samples
,
field
,
line
.
getSAMSequenceRecord
.
getSequenceName
)
}
writeGenotypeField
(
stats
,
prefix
,
samples
,
field
,
"total"
)
Map
(
record
.
getChr
->
buffer
.
toMap
,
"total"
->
buffer
.
toMap
)
}
/** Function to write 1 specific genotype field */
protected
def
writeGenotypeField
(
stats
:
Stats
,
prefix
:
String
,
samples
:
List
[
String
],
field
:
String
,
chr
:
String
)
:
Unit
=
{
val
file
=
new
File
(
prefix
+
"-"
+
chr
+
"-"
+
field
+
".tsv"
)
protected
def
writeGenotypeField
(
stats
:
Stats
,
samples
:
List
[
String
],
field
:
String
,
outputDir
:
File
,
prefix
:
String
=
""
,
chr
:
String
=
"total"
)
:
Unit
=
{
val
file
=
(
prefix
,
chr
)
match
{
case
(
""
,
"total"
)
=>
new
File
(
outputDir
,
field
+
".tsv"
)
case
(
_
,
"total"
)
=>
new
File
(
outputDir
,
prefix
+
"-"
+
field
+
".tsv"
)
case
(
""
,
_
)
=>
new
File
(
outputDir
,
chr
+
"-"
+
field
+
".tsv"
)
case
_
=>
new
File
(
outputDir
,
prefix
+
"-"
+
chr
+
"-"
+
field
+
".tsv"
)
}
file
.
getParentFile
.
mkdirs
()
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
samples
.
mkString
(
field
+
"\t"
,
"\t"
,
""
))
...
...
@@ -370,11 +435,19 @@ object VcfStats extends ToolCommand {
}
/** Function to write 1 specific general field */
protected
def
writeField
(
prefix
:
String
,
data
:
mutable.Map
[
Any
,
Int
])
:
File
=
{
val
file
=
new
File
(
commandArgs
.
outputDir
+
"/"
+
prefix
+
".tsv"
)
protected
def
writeField
(
stats
:
Stats
,
field
:
String
,
outputDir
:
File
,
prefix
:
String
=
""
,
chr
:
String
=
"total"
)
:
File
=
{
val
file
=
(
prefix
,
chr
)
match
{
case
(
""
,
"total"
)
=>
new
File
(
outputDir
,
field
+
".tsv"
)
case
(
_
,
"total"
)
=>
new
File
(
outputDir
,
prefix
+
"-"
+
field
+
".tsv"
)
case
(
""
,
_
)
=>
new
File
(
outputDir
,
chr
+
"-"
+
field
+
".tsv"
)
case
_
=>
new
File
(
outputDir
,
prefix
+
"-"
+
chr
+
"-"
+
field
+
".tsv"
)
}
val
data
=
stats
.
generalStats
.
getOrElse
(
chr
,
mutable
.
Map
[
String
,
mutable.Map
[
Any
,
Int
]]()).
getOrElse
(
field
,
mutable
.
Map
[
Any
,
Int
]())
file
.
getParentFile
.
mkdirs
()
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
"
\t"
+
prefix
)
writer
.
println
(
"
value\tcount"
)
for
(
key
<-
data
.
keySet
.
toList
.
sortWith
(
sortAnyAny
(
_
,
_
)))
{
writer
.
println
(
key
+
"\t"
+
data
(
key
))
}
...
...
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