#404 hard limit maximum assembly base quality to the max of 93 repres…

…entable by Sanger format fastq.
PapenfussLab · Dec 10, 2020 · af820da · af820da
1 parent f529c82
commit af820da
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diff --git a/src/main/java/au/edu/wehi/idsv/AssemblyFactory.java b/src/main/java/au/edu/wehi/idsv/AssemblyFactory.java
@@ -151,6 +151,9 @@ private static SAMRecord createAssemblySAMRecord(
 			record.setAttribute(SamTags.UNANCHORED, 1);
 		} else {
 			record.setReadBases(baseCalls);
+			for (int i = 0 ;i < baseQuals.length; i++) {
+				baseQuals[i] = (byte)Math.min((int)baseQuals[i] & 0xFF, 93);
+			}
 			record.setBaseQualities(baseQuals);
 			if (breakend.start != breakend.end) {
 				throw new IllegalArgumentException("Imprecisely anchored breakends not supported by this constructor");

diff --git a/src/test/java/au/edu/wehi/idsv/AssemblyFactoryTest.java b/src/test/java/au/edu/wehi/idsv/AssemblyFactoryTest.java
@@ -540,5 +540,12 @@ public void realignment_of_breakpoint_outside_of_contig_bounds_should_have_inexa
 		assertEquals(new BreakendSummary(0, BWD, 1), re.getBreakendSummary().localBreakend());
 		assertEquals(new BreakendSummary(1, FWD, 212, 202, 222), re.getBreakendSummary().remoteBreakend());
 	}
+	@Test
+	public void basequal_range_should_be_limited() {
+		SAMRecord r = AssemblyFactory.createAnchoredBreakend(
+				getContext(), AES(), new SequentialIdGenerator("asm"), BWD, null,null,
+				0, 1, 2, B("GTACC"), new byte[] { 92,93,(byte)254,-1,94 });
+		assertArrayEquals(new byte[] { 92, 93,93,93,93}, r.getBaseQualities());
+	}
 }