Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
ef03063d
Commit
ef03063d
authored
Dec 22, 2016
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Move method to vcfutils
parent
960476a7
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
46 additions
and
46 deletions
+46
-46
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
...n/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
+8
-22
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+0
-22
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
...s/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
+16
-2
biopet-utils/src/test/scala/VcfUtilsTest.scala
biopet-utils/src/test/scala/VcfUtilsTest.scala
+22
-0
No files found.
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @
ef03063d
...
...
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.tools.vcfstats
import
java.io.
{
File
,
FileOutputStream
,
PrintWriter
}
import
htsjdk.samtools.util.Interval
import
htsjdk.variant.variantcontext.
{
Allele
,
Genotype
,
VariantContext
}
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
}
import
nl.lumc.sasc.biopet.utils.
{
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
...
...
@@ -30,7 +30,7 @@ import scala.util.Random
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration._
import
scala.concurrent.
{
Await
,
Future
}
import
scala.concurrent.
{
Await
,
Future
}
/**
* This tool will generate statistics from a vcf file
...
...
@@ -223,7 +223,7 @@ object VcfStats extends ToolCommand {
val
genotype2
=
record
.
getGenotype
(
sample2
)
if
(
genotype
.
getAlleles
==
genotype2
.
getAlleles
)
stats
.
samplesStats
(
sample1
).
sampleToSample
(
sample2
).
genotypeOverlap
+=
1
stats
.
samplesStats
(
sample1
).
sampleToSample
(
sample2
).
alleleOverlap
+=
alleleOverlap
(
genotype
.
getAlleles
.
toList
,
genotype2
.
getAlleles
.
toList
)
stats
.
samplesStats
(
sample1
).
sampleToSample
(
sample2
).
alleleOverlap
+=
VcfUtils
.
alleleOverlap
(
genotype
.
getAlleles
.
toList
,
genotype2
.
getAlleles
.
toList
)
}
}
chunkCounter
+=
1
...
...
@@ -332,20 +332,6 @@ object VcfStats extends ToolCommand {
value
.
collect
{
case
x
=>
x
.
split
(
"\t"
)(
index
)
}
}
/** Give back the number of alleles that overlap */
def
alleleOverlap
(
g1
:
List
[
Allele
],
g2
:
List
[
Allele
],
start
:
Int
=
0
)
:
Int
=
{
if
(
g1
.
isEmpty
)
start
else
{
val
found
=
g2
.
contains
(
g1
.
head
)
val
g2tail
=
if
(
found
)
{
val
index
=
g2
.
indexOf
(
g1
.
head
)
g2
.
drop
(
index
+
1
)
++
g2
.
take
(
index
)
}
else
g2
alleleOverlap
(
g1
.
tail
,
g2tail
,
if
(
found
)
start
+
1
else
start
)
}
}
protected
[
tools
]
def
fillGeneral
(
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
...
...
@@ -355,7 +341,7 @@ object VcfStats extends ToolCommand {
else
buffer
+=
key
->
(
map
+
(
value
->
map
.
getOrElse
(
value
,
0
)))
}
buffer
+=
"QUAL"
->
Map
(
"not set"
->
1
)
addToBuffer
(
"QUAL"
,
"not set"
,
false
)
addToBuffer
(
"SampleDistribution-Het"
,
"not set"
,
found
=
false
)
addToBuffer
(
"SampleDistribution-HetNonRef"
,
"not set"
,
found
=
false
)
...
...
@@ -464,10 +450,10 @@ object VcfStats extends ToolCommand {
else
buffer
+=
key
->
(
map
+
(
value
->
map
.
getOrElse
(
value
,
0
)))
}
buffer
+=
"DP"
->
Map
(
"not set"
->
1
)
buffer
+=
"GQ"
->
Map
(
"not set"
->
1
)
addToBuffer
(
"DP"
,
"not set"
,
false
)
addToBuffer
(
"GQ"
,
"not set"
,
false
)
addToBuffer
(
"general"
,
"Total"
,
f
ound
=
tru
e
)
addToBuffer
(
"general"
,
"Total"
,
f
als
e
)
addToBuffer
(
"general"
,
"Het"
,
false
)
addToBuffer
(
"general"
,
"HetNonRef"
,
false
)
addToBuffer
(
"general"
,
"Hom"
,
false
)
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
ef03063d
...
...
@@ -103,28 +103,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
s1
.
genotypeStats
.
getOrElse
(
"chr"
,
mutable
.
Map
[
String
,
mutable.Map
[
Any
,
Int
]]())
shouldBe
mutable
.
Map
(
"1"
->
mutable
.
Map
(
1
->
2
),
"2"
->
mutable
.
Map
(
2
->
8
))
}
@Test
def
testAlleleOverlap
()
:
Unit
=
{
val
a1
=
Allele
.
create
(
"G"
)
val
a2
=
Allele
.
create
(
"A"
)
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a1
,
a1
))
shouldBe
2
alleleOverlap
(
List
(
a2
,
a2
),
List
(
a2
,
a2
))
shouldBe
2
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a1
,
a2
))
shouldBe
2
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a2
,
a1
))
shouldBe
2
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a1
,
a2
))
shouldBe
2
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a2
,
a1
))
shouldBe
2
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a1
,
a1
))
shouldBe
1
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a1
,
a1
))
shouldBe
1
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a1
,
a2
))
shouldBe
1
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a2
,
a1
))
shouldBe
1
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a2
,
a2
))
shouldBe
0
alleleOverlap
(
List
(
a2
,
a2
),
List
(
a1
,
a1
))
shouldBe
0
}
@Test
def
testMergeStatsMap
=
{
val
m1
:
mutable.Map
[
Any
,
Int
]
=
mutable
.
Map
(
"a"
->
1
)
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
View file @
ef03063d
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.utils
import
java.io.File
import
java.util
import
htsjdk.variant.variantcontext.
{
Genotype
,
VariantContext
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFHeader
,
VCFFilterHeaderLine
}
import
htsjdk.variant.variantcontext.
{
Allele
,
Genotype
,
VariantContext
}
import
htsjdk.variant.vcf.
{
VCFFileReader
,
VCFFilterHeaderLine
,
VCFHeader
}
import
scala.collection.JavaConversions._
...
...
@@ -149,4 +149,18 @@ object VcfUtils {
def
isCompoundNoCall
(
genotype
:
Genotype
)
:
Boolean
=
{
genotype
.
isCalled
&&
genotype
.
getAlleles
.
exists
(
_
.
isNoCall
)
&&
genotype
.
getAlleles
.
exists
(
_
.
isReference
)
}
/** Give back the number of alleles that overlap */
def
alleleOverlap
(
g1
:
List
[
Allele
],
g2
:
List
[
Allele
],
start
:
Int
=
0
)
:
Int
=
{
if
(
g1
.
isEmpty
)
start
else
{
val
found
=
g2
.
contains
(
g1
.
head
)
val
g2tail
=
if
(
found
)
{
val
index
=
g2
.
indexOf
(
g1
.
head
)
g2
.
drop
(
index
+
1
)
++
g2
.
take
(
index
)
}
else
g2
alleleOverlap
(
g1
.
tail
,
g2tail
,
if
(
found
)
start
+
1
else
start
)
}
}
}
biopet-utils/src/test/scala/VcfUtilsTest.scala
View file @
ef03063d
...
...
@@ -27,4 +27,26 @@ class VcfUtilsTest extends TestNGSuite with Matchers {
VcfUtils
.
isCompoundNoCall
(
completeNoCall
)
shouldBe
false
}
@Test
def
testAlleleOverlap
()
:
Unit
=
{
val
a1
=
Allele
.
create
(
"G"
)
val
a2
=
Allele
.
create
(
"A"
)
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a1
,
a1
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a2
,
a2
),
List
(
a2
,
a2
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a1
,
a2
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a2
,
a1
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a1
,
a2
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a2
,
a1
))
shouldBe
2
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a2
),
List
(
a1
,
a1
))
shouldBe
1
VcfUtils
.
alleleOverlap
(
List
(
a2
,
a1
),
List
(
a1
,
a1
))
shouldBe
1
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a1
,
a2
))
shouldBe
1
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a2
,
a1
))
shouldBe
1
VcfUtils
.
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a2
,
a2
))
shouldBe
0
VcfUtils
.
alleleOverlap
(
List
(
a2
,
a2
),
List
(
a1
,
a1
))
shouldBe
0
}
}
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment