From 3728786b4d6fbe439a0fd1fde28f9c2a94648e28 Mon Sep 17 00:00:00 2001 From: ekaterina_kazachkova Date: Mon, 10 Apr 2017 17:00:37 +0300 Subject: [PATCH] replace method getRefPos() into abstract class EdgingRecordAndOffset and delete constructor in AbstractRecordAndOffset --- .../htsjdk/samtools/util/AbstractRecordAndOffset.java | 17 ----------------- .../htsjdk/samtools/util/EdgingRecordAndOffset.java | 2 ++ .../samtools/util/AbstractRecordAndOffsetTest.java | 3 +-- 3 files changed, 3 insertions(+), 19 deletions(-) diff --git a/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java b/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java index 28b9d34b3..e76b66683 100644 --- a/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java +++ b/src/main/java/htsjdk/samtools/util/AbstractRecordAndOffset.java @@ -49,16 +49,6 @@ /** * @param record inner SAMRecord * @param offset from the start of the read - * @param length of alignment block - * @param refPos corresponding to read offset reference position - */ - public AbstractRecordAndOffset(final SAMRecord record, final int offset, int length, int refPos) { - this(record, offset); - } - - /** - * @param record inner SAMRecord - * @param offset from the start of the read */ public AbstractRecordAndOffset(final SAMRecord record, final int offset) { this.offset = offset; @@ -94,13 +84,6 @@ public int getLength() { } /** - * @return the position in reference sequence, to which the start of alignment block is aligned. - */ - public int getRefPos() { - return -1; - } - - /** * @return read name of inner SAMRecord. */ public String getReadName() { diff --git a/src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java b/src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java index 85beb66f0..df282b00f 100644 --- a/src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java +++ b/src/main/java/htsjdk/samtools/util/EdgingRecordAndOffset.java @@ -56,6 +56,8 @@ private EdgingRecordAndOffset(SAMRecord record, int offset) { public abstract byte getBaseQuality(int position); + public abstract int getRefPos(); + public static EdgingRecordAndOffset createBeginRecord(SAMRecord record, int offset, int length, int refPos) { return new StartEdgingRecordAndOffset(record, offset, length, refPos); } diff --git a/src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java b/src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java index 568c84c7c..55ae505bf 100644 --- a/src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java +++ b/src/test/java/htsjdk/samtools/util/AbstractRecordAndOffsetTest.java @@ -52,12 +52,11 @@ public void setUp(){ @Test public void testConstructor(){ - AbstractRecordAndOffset abstractRecordAndOffset = new AbstractRecordAndOffset(record, 0, 10, 3); + AbstractRecordAndOffset abstractRecordAndOffset = new AbstractRecordAndOffset(record, 0); assertArrayEquals(qualities, abstractRecordAndOffset.getBaseQualities()); assertArrayEquals(bases, abstractRecordAndOffset.getRecord().getReadBases()); assertEquals('A', abstractRecordAndOffset.getReadBase()); assertEquals(30, abstractRecordAndOffset.getBaseQuality()); assertEquals(0, abstractRecordAndOffset.getOffset()); - assertEquals(-1, abstractRecordAndOffset.getRefPos()); } }