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Mirrors
biopet.biopet
Commits
11a6c2db
Commit
11a6c2db
authored
Feb 04, 2015
by
Peter van 't Hof
Browse files
Added general stats
parent
612be8f7
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
11a6c2db
...
...
@@ -114,15 +114,17 @@ object VcfStats extends ToolCommand {
val
samples
=
header
.
getSampleNamesInOrder
.
toList
val
intervals
:
List
[
Interval
]
=
(
for
(
seq
<-
header
.
getSequenceDictionary
.
getSequences
;
for
(
seq
<-
header
.
getSequenceDictionary
.
getSequences
;
chunks
=
seq
.
getSequenceLength
/
10000000
;
i
<-
1
until
chunks
)
yield
{
i
<-
1
until
chunks
)
yield
{
val
size
=
seq
.
getSequenceLength
/
chunks
val
begin
=
size
*
(
i
-
1
)
+
1
val
begin
=
size
*
(
i
-
1
)
+
1
val
end
=
if
(
i
>=
chunks
)
seq
.
getSequenceLength
else
size
*
i
new
Interval
(
seq
.
getSequenceName
,
begin
,
end
)
}
).
toList
).
toList
val
totalBases
=
intervals
.
foldRight
(
0L
)(
_
.
length
()
+
_
)
...
...
@@ -144,7 +146,7 @@ object VcfStats extends ToolCommand {
var
variantCounter
=
0L
var
baseCounter
=
0L
def
status
(
count
:
Int
,
interval
:
Interval
)
:
Unit
=
{
def
status
(
count
:
Int
,
interval
:
Interval
)
:
Unit
=
{
variantCounter
+=
count
baseCounter
+=
interval
.
length
()
val
fraction
=
baseCounter
.
toFloat
/
totalBases
*
100
...
...
@@ -158,8 +160,9 @@ object VcfStats extends ToolCommand {
val
stats
=
createStats
logger
.
info
(
"Starting on: "
+
interval
)
for
(
record
<-
reader
.
query
(
interval
.
getSequence
,
interval
.
getStart
,
interval
.
getEnd
)
if
record
.
getStart
<=
interval
.
getEnd
)
{
for
(
record
<-
reader
.
query
(
interval
.
getSequence
,
interval
.
getStart
,
interval
.
getEnd
)
if
record
.
getStart
<=
interval
.
getEnd
)
{
mergeNestedStatsMap
(
stats
.
generalStats
,
checkGeneral
(
record
))
for
(
sample1
<-
samples
)
yield
{
val
genotype
=
record
.
getGenotype
(
sample1
)
...
...
@@ -201,13 +204,25 @@ object VcfStats extends ToolCommand {
buffer
+=
"DP"
->
Map
((
if
(
genotype
.
hasDP
)
genotype
.
getDP
else
"not set"
)
->
1
)
buffer
+=
"GQ"
->
Map
((
if
(
genotype
.
hasGQ
)
genotype
.
getGQ
else
"not set"
)
->
1
)
def
addToBuffer
(
key
:
String
,
value
:
Any
)
:
Unit
=
{
def
addToBuffer
(
key
:
String
,
value
:
Any
)
:
Unit
=
{
val
map
=
buffer
.
getOrElse
(
key
,
Map
())
buffer
+=
key
->
(
map
+
(
value
->
(
map
.
getOrElse
(
value
,
0
)
+
1
)))
}
val
usedAlleles
=
(
for
(
allele
<-
genotype
.
getAlleles
)
yield
record
.
getAlleleIndex
(
allele
)).
toList
if
(
genotype
.
isHet
)
addToBuffer
(
"general"
,
"Het"
)
if
(
genotype
.
isHetNonRef
)
addToBuffer
(
"general"
,
"HetNonRef"
)
if
(
genotype
.
isHom
)
addToBuffer
(
"general"
,
"Hom"
)
if
(
genotype
.
isHomRef
)
addToBuffer
(
"general"
,
"HomRef"
)
if
(
genotype
.
isHomVar
)
addToBuffer
(
"general"
,
"HomVar"
)
if
(
genotype
.
isMixed
)
addToBuffer
(
"general"
,
"Mixed"
)
if
(
genotype
.
isNoCall
)
addToBuffer
(
"general"
,
"NoCall"
)
if
(
genotype
.
isNonInformative
)
addToBuffer
(
"general"
,
"NonInformative"
)
if
(
genotype
.
isAvailable
)
addToBuffer
(
"general"
,
"Available"
)
if
(
genotype
.
isCalled
)
addToBuffer
(
"general"
,
"Called"
)
if
(
genotype
.
isFiltered
)
addToBuffer
(
"general"
,
"Filtered"
)
if
(
genotype
.
hasAD
)
{
val
ad
=
genotype
.
getAD
for
(
i
<-
0
until
ad
.
size
if
ad
(
i
)
>
0
)
{
...
...
@@ -218,21 +233,20 @@ object VcfStats extends ToolCommand {
else
addToBuffer
(
"AD-not_used"
,
ad
(
i
))
}
}
buffer
.
toMap
}
def
writeGenotypeFields
(
stats
:
Stats
,
prefix
:
String
,
samples
:
List
[
String
])
{
val
fields
=
List
(
"DP"
,
"GQ"
,
"AD"
,
"AD-ref"
,
"AD-alt"
,
"AD-used"
,
"AD-not_used"
)
val
fields
=
List
(
"DP"
,
"GQ"
,
"AD"
,
"AD-ref"
,
"AD-alt"
,
"AD-used"
,
"AD-not_used"
,
"general"
)
for
(
field
<-
fields
)
{
val
file
=
new
File
(
prefix
+
field
+
".tsv"
)
file
.
getParentFile
.
mkdirs
()
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
samples
.
mkString
(
"\t"
,
"\t"
,
""
))
val
keySet
=
(
for
(
sample
<-
samples
)
yield
stats
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
field
,
Map
[
Any
,
Int
]()).
keySet
).
fold
(
Set
[
Any
]())(
_
++
_
)
val
keySet
=
(
for
(
sample
<-
samples
)
yield
stats
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
field
,
Map
[
Any
,
Int
]()).
keySet
).
fold
(
Set
[
Any
]())(
_
++
_
)
for
(
key
<-
keySet
.
toList
.
sortWith
(
sortAnyAny
(
_
,
_
)))
{
val
values
=
for
(
sample
<-
samples
)
yield
stats
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
field
,
Map
[
Any
,
Int
]()).
getOrElse
(
key
,
0
)
val
values
=
for
(
sample
<-
samples
)
yield
stats
.
samplesStats
(
sample
).
genotypeStats
.
getOrElse
(
field
,
Map
[
Any
,
Int
]()).
getOrElse
(
key
,
0
)
writer
.
println
(
values
.
mkString
(
key
+
"\t"
,
"\t"
,
""
))
}
writer
.
close
()
...
...
@@ -315,9 +329,9 @@ object VcfStats extends ToolCommand {
logger
.
info
(
"Starting: "
+
command
)
val
process
=
Process
(
command
).
run
(
ProcessLogger
(
x
=>
logger
.
debug
(
x
),
x
=>
logger
.
debug
(
x
)))
if
(
process
.
exitValue
()
==
0
)
logger
.
info
(
"Done: "
+
command
)
if
(
process
.
exitValue
()
==
0
)
logger
.
info
(
"Done: "
+
command
)
else
{
logger
.
warn
(
"Failed: "
+
command
)
logger
.
warn
(
"Failed: "
+
command
)
if
(!
logger
.
isDebugEnabled
)
logger
.
warn
(
"Use -l debug for more info"
)
}
}
...
...
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