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biopet.biopet
Commits
51d189aa
Commit
51d189aa
authored
Apr 14, 2015
by
Peter van 't Hof
Browse files
Adding placeholder for RNA and Target stats
parent
0c9b920b
Changes
6
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
0 → 100644
View file @
51d189aa
#{ //TODO: Need content }#
Todo
\ No newline at end of file
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
0 → 100644
View file @
51d189aa
#{ //TODO: Need content }#
Todo
\ No newline at end of file
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
51d189aa
package
nl.lumc.sasc.biopet.pipelines.bammetrics
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportPage
,
ReportSection
}
/**
* Created by pjvan_thof on 3/30/15.
...
...
@@ -22,8 +22,10 @@ object BammetricsReport extends ReportBuilder {
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"Bam Stats"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"
),
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
),
"RNA (optional)"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp"
),
"Target (optional)"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp"
),
"GC Bias"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp"
)
),
),
Map
()
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
View file @
51d189aa
...
...
@@ -66,7 +66,7 @@ object VcfToTsv extends ToolCommand {
opt
[
String
](
"list_separator"
)
maxOccurs
(
1
)
action
{
(
x
,
c
)
=>
c
.
copy
(
listSeparator
=
x
)
}
text
(
"Optional list separator. By default, lists are separated by a comma"
)
opt
[
Int
](
"max_decimals"
)
maxOccurs
(
1
)
action
{
(
x
,
c
)
=>
opt
[
Int
](
"max_decimals"
)
maxOccurs
(
1
)
action
{
(
x
,
c
)
=>
c
.
copy
(
maxDecimals
=
x
)
}
text
(
"Number of decimal places for numbers. Default is 2"
)
}
...
...
@@ -79,7 +79,7 @@ object VcfToTsv extends ToolCommand {
// Throw exception if separator and listSeparator are identical
if
(
commandArgs
.
separator
==
commandArgs
.
listSeparator
)
throw
new
IllegalArgumentException
(
"Separator and list_separator should not be identical"
"Separator and list_separator should not be identical"
)
val
formatter
=
createFormatter
(
commandArgs
.
maxDecimals
)
...
...
@@ -101,7 +101,6 @@ object VcfToTsv extends ToolCommand {
buffer
.
toSet
[
String
]
}
val
sortedFields
=
sortFields
(
fields
,
samples
.
toList
)
val
writer
=
if
(
commandArgs
.
outputFile
!=
null
)
new
PrintStream
(
commandArgs
.
outputFile
)
...
...
@@ -137,10 +136,10 @@ object VcfToTsv extends ToolCommand {
val
l
=
for
(
g
<-
genotype
.
getAlleles
)
yield
vcfRecord
.
getAlleleIndex
(
g
)
l
.
map
(
x
=>
if
(
x
<
0
)
"."
else
x
).
mkString
(
"/"
)
}
if
(
genotype
.
hasAD
)
values
+=
sample
+
"-AD"
->
List
(
genotype
.
getAD
:
_
*
).
mkString
(
commandArgs
.
listSeparator
)
if
(
genotype
.
hasDP
)
values
+=
sample
+
"-DP"
->
genotype
.
getDP
if
(
genotype
.
hasGQ
)
values
+=
sample
+
"-GQ"
->
genotype
.
getGQ
if
(
genotype
.
hasPL
)
values
+=
sample
+
"-PL"
->
List
(
genotype
.
getPL
:
_
*
).
mkString
(
commandArgs
.
listSeparator
)
if
(
genotype
.
hasAD
)
values
+=
sample
+
"-AD"
->
List
(
genotype
.
getAD
:
_
*
).
mkString
(
commandArgs
.
listSeparator
)
if
(
genotype
.
hasDP
)
values
+=
sample
+
"-DP"
->
genotype
.
getDP
if
(
genotype
.
hasGQ
)
values
+=
sample
+
"-GQ"
->
genotype
.
getGQ
if
(
genotype
.
hasPL
)
values
+=
sample
+
"-PL"
->
List
(
genotype
.
getPL
:
_
*
).
mkString
(
commandArgs
.
listSeparator
)
for
((
field
,
content
)
<-
genotype
.
getExtendedAttributes
)
{
values
+=
sample
+
"-"
+
field
->
content
}
...
...
@@ -164,7 +163,6 @@ object VcfToTsv extends ToolCommand {
new
DecimalFormat
(
patternString
)
}
/**
* This fields sorts fields, such that non-info and non-sample specific fields (e.g. general ones) are on front
* followed by info fields
...
...
@@ -182,7 +180,7 @@ object VcfToTsv extends ToolCommand {
fields
.
toList
.
sortWith
((
a
,
b
)
=>
{
(
fieldType
(
a
),
fieldType
(
b
))
match
{
case
(
'g'
,
'g'
)
=>
{
case
(
'g'
,
'g'
)
=>
{
val
ai
=
defaultFields
.
indexOf
(
a
)
val
bi
=
defaultFields
.
indexOf
(
b
)
if
(
bi
<
0
)
true
else
ai
<=
bi
...
...
@@ -191,16 +189,16 @@ object VcfToTsv extends ToolCommand {
val
sampleA
=
a
.
split
(
"-"
).
head
val
sampleB
=
b
.
split
(
"-"
).
head
sampleA
.
compareTo
(
sampleB
)
match
{
case
0
=>
!(
a
.
compareTo
(
b
)
>
0
)
case
0
=>
!(
a
.
compareTo
(
b
)
>
0
)
case
i
if
(
i
>
0
)
=>
false
case
_
=>
true
case
_
=>
true
}
}
case
(
'g'
,
_
)
=>
true
case
(
_
,
'g'
)
=>
false
case
(
'g'
,
_
)
=>
true
case
(
_
,
'g'
)
=>
false
case
(
a
,
b
)
if
a
==
b
=>
!(
a
.
compareTo
(
b
)
>
0
)
case
(
'i'
,
_
)
=>
true
case
_
=>
false
case
(
'i'
,
_
)
=>
true
case
_
=>
false
}
})
}
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
View file @
51d189aa
...
...
@@ -64,7 +64,7 @@ class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
val
sorted
=
sortFields
(
unsortedFields
,
samples
)
sorted
should
be
(
List
(
"WeirdField"
,
"INFO-AlleleScoreSomething"
,
"INFO-ScoreSomething"
,
"INFO-Something"
,
"Child01-GT"
,
"Father03-GT"
,
"Mother02-GT"
))
"Child01-GT"
,
"Father03-GT"
,
"Mother02-GT"
))
}
}
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
51d189aa
...
...
@@ -19,17 +19,17 @@ object FlexiprepReport extends ReportBuilder {
def
flexiprepPage
=
ReportPage
(
Map
(),
List
(
"Read Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"Base Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
),
fastqcPlotSection
(
"Base quality"
,
"plot_per_base_quality"
),
fastqcPlotSection
(
"Sequence quality"
,
"plot_per_sequence_quality"
),
fastqcPlotSection
(
"Base GC content"
,
"plot_per_base_gc_content"
),
fastqcPlotSection
(
"Sequence GC content"
,
"plot_per_sequence_gc_content"
),
fastqcPlotSection
(
"Base seqeunce content"
,
"plot_per_base_sequence_content"
),
fastqcPlotSection
(
"Duplication"
,
"plot_duplication_levels"
),
fastqcPlotSection
(
"Kmers"
,
"plot_kmer_profiles"
),
fastqcPlotSection
(
"Length distribution"
,
"plot_sequence_length_distribution"
)
),
"Read Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"Base Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
),
fastqcPlotSection
(
"Base quality"
,
"plot_per_base_quality"
),
fastqcPlotSection
(
"Sequence quality"
,
"plot_per_sequence_quality"
),
fastqcPlotSection
(
"Base GC content"
,
"plot_per_base_gc_content"
),
fastqcPlotSection
(
"Sequence GC content"
,
"plot_per_sequence_gc_content"
),
fastqcPlotSection
(
"Base seqeunce content"
,
"plot_per_base_sequence_content"
),
fastqcPlotSection
(
"Duplication"
,
"plot_duplication_levels"
),
fastqcPlotSection
(
"Kmers"
,
"plot_kmer_profiles"
),
fastqcPlotSection
(
"Length distribution"
,
"plot_sequence_length_distribution"
)
),
Map
()
)
...
...
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