Commit 50bb1535 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Format fix

parent 1579a88b
...@@ -41,19 +41,19 @@ class FlagstatCollector { ...@@ -41,19 +41,19 @@ class FlagstatCollector {
} }
/** /**
* The method will aditional checks based on mapping quality of the sam records. * The method will aditional checks based on mapping quality of the sam records.
* *
* @param m steps of qaulity * @param m steps of qaulity
* @param max maximum quality * @param max maximum quality
*/ */
def loadQualityFunctions(m: Int = 10, max: Int = 60): Unit = { def loadQualityFunctions(m: Int = 10, max: Int = 60): Unit = {
for (t <- 0 to (max / m)) for (t <- 0 to (max / m))
this.addFunction("MAPQ>" + (t * m), record => record.getMappingQuality > (t * 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 = { def loadOrientationFunctions = {
this.addFunction("First normal, second read inverted (paired end orientation)", record => { this.addFunction("First normal, second read inverted (paired end orientation)", record => {
if (record.getReadPairedFlag && if (record.getReadPairedFlag &&
......
...@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite ...@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test 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 { class BamStatsTest extends TestNGSuite with Matchers {
@Test @Test
def testMain: Unit = { def testMain: Unit = {
......
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