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biopet.biopet
Commits
50bb1535
Commit
50bb1535
authored
Jul 21, 2016
by
Peter van 't Hof
Browse files
Format fix
parent
1579a88b
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
View file @
50bb1535
...
...
@@ -41,19 +41,19 @@ class FlagstatCollector {
}
/**
* The method will aditional checks based on mapping quality of the sam records.
*
* @param m steps of qaulity
* @param max maximum quality
*/
* The method will aditional checks based on mapping quality of the sam records.
*
* @param m steps of qaulity
* @param max maximum quality
*/
def
loadQualityFunctions
(
m
:
Int
=
10
,
max
:
Int
=
60
)
:
Unit
=
{
for
(
t
<-
0
to
(
max
/
m
))
this
.
addFunction
(
"MAPQ>"
+
(
t
*
m
),
record
=>
record
.
getMappingQuality
>
(
t
*
m
))
}
/**
* This method will add functions to check orientation, for this a combination of flags and read positions are used.
*/
* This method will add functions to check orientation, for this a combination of flags and read positions are used.
*/
def
loadOrientationFunctions
=
{
this
.
addFunction
(
"First normal, second read inverted (paired end orientation)"
,
record
=>
{
if
(
record
.
getReadPairedFlag
&&
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
View file @
50bb1535
...
...
@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 21-7-16.
*/
* Created by pjvan_thof on 21-7-16.
*/
class
BamStatsTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testMain
:
Unit
=
{
...
...
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