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biopet.biopet
Commits
ed129189
Commit
ed129189
authored
Jul 21, 2016
by
Peter van 't Hof
Browse files
Remove duplicated stats
parent
99f13260
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
View file @
ed129189
...
...
@@ -94,8 +94,6 @@ object BamStats extends ToolCommand {
val
stats
=
waitOnFutures
(
unmappedFuture
::
contigsFutures
.
toList
)
logger
.
info
(
s
"total: ${stats.totalReads}, unmapped: ${stats.unmapped}, secondary: ${stats.secondary}"
)
stats
.
writeStatsToFiles
(
outputDir
)
}
...
...
@@ -167,10 +165,7 @@ object BamStats extends ToolCommand {
// Read based stats
if
(
samRecord
.
getAlignmentStart
>
threadStart
&&
samRecord
.
getAlignmentStart
<=
threadEnd
)
{
totalStats
.
flagstat
.
loadRecord
(
samRecord
)
totalStats
.
totalReads
+=
1
if
(
samRecord
.
isSecondaryOrSupplementary
)
totalStats
.
secondary
+=
1
if
(
samRecord
.
getReadUnmappedFlag
)
totalStats
.
unmapped
+=
1
else
{
// Mapped read
if
(!
samRecord
.
getReadUnmappedFlag
)
{
// Mapped read
totalStats
.
mappingQualityHistogram
.
add
(
samRecord
.
getMappingQuality
)
}
if
(
samRecord
.
getProperPairFlag
&&
samRecord
.
getFirstOfPairFlag
&&
!
samRecord
.
getSecondOfPairFlag
)
...
...
@@ -212,8 +207,6 @@ object BamStats extends ToolCommand {
val
samReader
=
SamReaderFactory
.
makeDefault
().
open
(
bamFile
)
for
(
samRecord
<-
samReader
.
queryUnmapped
())
{
stats
.
flagstat
.
loadRecord
(
samRecord
)
stats
.
totalReads
+=
1
stats
.
unmapped
+=
1
}
samReader
.
close
()
stats
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
View file @
ed129189
...
...
@@ -7,10 +7,7 @@ import nl.lumc.sasc.biopet.tools.flagstat.FlagstatCollector
/**
* Created by pjvanthof on 05/07/16.
*/
case
class
Stats
(
var
totalReads
:
Long
=
0L
,
var
unmapped
:
Long
=
0L
,
var
secondary
:
Long
=
0L
,
flagstat
:
FlagstatCollector
=
new
FlagstatCollector
(),
case
class
Stats
(
flagstat
:
FlagstatCollector
=
new
FlagstatCollector
(),
mappingQualityHistogram
:
Histogram
[
Int
]
=
new
Histogram
[
Int
](),
insertSizeHistogram
:
Histogram
[
Int
]
=
new
Histogram
[
Int
](),
clippingHistogram
:
Histogram
[
Int
]
=
new
Histogram
[
Int
](),
...
...
@@ -24,8 +21,6 @@ case class Stats(var totalReads: Long = 0L,
/** This will add an other [[Stats]] inside `this` */
def
+=
(
other
:
Stats
)
:
Stats
=
{
this
.
totalReads
+=
other
.
totalReads
this
.
unmapped
+=
other
.
unmapped
this
.
flagstat
+=
other
.
flagstat
this
.
mappingQualityHistogram
+=
other
.
mappingQualityHistogram
this
.
insertSizeHistogram
+=
other
.
insertSizeHistogram
...
...
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