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biopet.biopet
Commits
7d77c4c1
Commit
7d77c4c1
authored
Jun 10, 2016
by
Sander Bollen
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attempt to fix vcfstats so that it will always output something, even if there are 0 variants
parent
d5d6a13d
Changes
2
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2 changed files
with
100 additions
and
2 deletions
+100
-2
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
+1
-1
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+99
-1
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
View file @
7d77c4c1
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
Input
}
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
def
analysis_type
=
"BaseRecalibrator"
scatterClass
=
classOf
[
ContigScatterFunction
]
setupScatterFunction
=
{
case
scatter
:
GATKScatterFunction
=>
scatter
.
includeUnmapped
=
false
}
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
7d77c4c1
...
...
@@ -281,8 +281,17 @@ object VcfStats extends ToolCommand {
val
stats
=
createStats
logger
.
info
(
"Starting on: "
+
interval
)
val
query
=
reader
.
query
(
interval
.
getContig
,
interval
.
getStart
,
interval
.
getEnd
)
if
(!
query
.
hasNext
)
{
mergeNestedStatsMap
(
stats
.
generalStats
,
fillGeneral
(
adInfoTags
))
for
(
sample
<-
samples
)
yield
{
mergeNestedStatsMap
(
stats
.
samplesStats
(
sample
).
genotypeStats
,
fillGenotype
(
adGenotypeTags
))
}
chunkCounter
+=
1
}
for
(
record
<-
reader
.
query
(
interval
.
getContig
,
interval
.
getStart
,
interval
.
getEnd
)
if
record
.
getStart
<=
interval
.
getEnd
record
<-
query
if
record
.
getStart
<=
interval
.
getEnd
)
{
mergeNestedStatsMap
(
stats
.
generalStats
,
checkGeneral
(
record
,
adInfoTags
))
for
(
sample1
<-
samples
)
yield
{
...
...
@@ -414,6 +423,59 @@ object VcfStats extends ToolCommand {
}
}
protected
[
tools
]
def
fillGeneral
(
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
=
{
val
map
=
buffer
.
getOrElse
(
key
,
Map
())
if
(
found
)
buffer
+=
key
->
(
map
+
(
value
->
(
map
.
getOrElse
(
value
,
0
)
+
1
)))
else
buffer
+=
key
->
(
map
+
(
value
->
map
.
getOrElse
(
value
,
0
)))
}
buffer
+=
"QUAL"
->
Map
(
0
->
1
)
addToBuffer
(
"SampleDistribution-Het"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-HetNonRef"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Hom"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-HomRef"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-HomVar"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Mixed"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-NoCall"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-NonInformative"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Available"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Called"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Filtered"
,
0
,
found
=
false
)
addToBuffer
(
"SampleDistribution-Variant"
,
0
,
found
=
false
)
addToBuffer
(
"general"
,
"Total"
,
found
=
true
)
addToBuffer
(
"general"
,
"Biallelic"
,
false
)
addToBuffer
(
"general"
,
"ComplexIndel"
,
false
)
addToBuffer
(
"general"
,
"Filtered"
,
false
)
addToBuffer
(
"general"
,
"FullyDecoded"
,
false
)
addToBuffer
(
"general"
,
"Indel"
,
false
)
addToBuffer
(
"general"
,
"Mixed"
,
false
)
addToBuffer
(
"general"
,
"MNP"
,
false
)
addToBuffer
(
"general"
,
"MonomorphicInSamples"
,
false
)
addToBuffer
(
"general"
,
"NotFiltered"
,
false
)
addToBuffer
(
"general"
,
"PointEvent"
,
false
)
addToBuffer
(
"general"
,
"PolymorphicInSamples"
,
false
)
addToBuffer
(
"general"
,
"SimpleDeletion"
,
false
)
addToBuffer
(
"general"
,
"SimpleInsertion"
,
false
)
addToBuffer
(
"general"
,
"SNP"
,
false
)
addToBuffer
(
"general"
,
"StructuralIndel"
,
false
)
addToBuffer
(
"general"
,
"Symbolic"
,
false
)
addToBuffer
(
"general"
,
"SymbolicOrSV"
,
false
)
addToBuffer
(
"general"
,
"Variant"
,
false
)
val
skipTags
=
List
(
"QUAL"
,
"general"
)
for
(
tag
<-
additionalTags
if
!
skipTags
.
contains
(
tag
))
{
addToBuffer
(
tag
,
0
,
found
=
false
)
}
Map
(
"total"
->
buffer
.
toMap
)
}
/** Function to check all general stats, all info expect sample/genotype specific stats */
protected
[
tools
]
def
checkGeneral
(
record
:
VariantContext
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
...
...
@@ -470,6 +532,42 @@ object VcfStats extends ToolCommand {
Map
(
record
.
getContig
->
buffer
.
toMap
,
"total"
->
buffer
.
toMap
)
}
protected
[
tools
]
def
fillGenotype
(
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
=
{
val
map
=
buffer
.
getOrElse
(
key
,
Map
())
if
(
found
)
buffer
+=
key
->
(
map
+
(
value
->
(
map
.
getOrElse
(
value
,
0
)
+
1
)))
else
buffer
+=
key
->
(
map
+
(
value
->
map
.
getOrElse
(
value
,
0
)))
}
buffer
+=
"DP"
->
Map
(
"not set"
->
1
)
buffer
+=
"GQ"
->
Map
(
"not set"
->
1
)
addToBuffer
(
"general"
,
"Total"
,
found
=
true
)
addToBuffer
(
"general"
,
"Het"
,
false
)
addToBuffer
(
"general"
,
"HetNonRef"
,
false
)
addToBuffer
(
"general"
,
"Hom"
,
false
)
addToBuffer
(
"general"
,
"HomRef"
,
false
)
addToBuffer
(
"general"
,
"HomVar"
,
false
)
addToBuffer
(
"general"
,
"Mixed"
,
false
)
addToBuffer
(
"general"
,
"NoCall"
,
false
)
addToBuffer
(
"general"
,
"NonInformative"
,
false
)
addToBuffer
(
"general"
,
"Available"
,
false
)
addToBuffer
(
"general"
,
"Called"
,
false
)
addToBuffer
(
"general"
,
"Filtered"
,
false
)
addToBuffer
(
"general"
,
"Variant"
,
false
)
val
skipTags
=
List
(
"DP"
,
"GQ"
,
"AD"
,
"AD-ref"
,
"AD-alt"
,
"AD-used"
,
"AD-not_used"
,
"general"
)
for
(
tag
<-
additionalTags
if
!
skipTags
.
contains
(
tag
))
{
addToBuffer
(
tag
,
0
,
found
=
false
)
}
Map
(
"total"
->
buffer
.
toMap
)
}
/** Function to check sample/genotype specific stats */
protected
[
tools
]
def
checkGenotype
(
record
:
VariantContext
,
genotype
:
Genotype
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
...
...
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