New CLP to clip homopolymer starting sequence

broadinstitute · Jan 7, 2025 · 32df00c · 32df00c
1 parent 714301e
commit 32df00c
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Showing 6 changed files with 116 additions and 16 deletions.
diff --git a/src/java/org/broadinstitute/dropseqrna/readtrimming/TrimHomopolymerStartingSequence.java b/src/java/org/broadinstitute/dropseqrna/readtrimming/TrimHomopolymerStartingSequence.java
@@ -43,6 +43,7 @@
         programGroup = DropSeq.class)
 public class TrimHomopolymerStartingSequence
 extends AbstractTrimmerClp {
+    public static final byte FULL_TRIM_QUALITY_SCORE = 3;
     private final Log log = Log.getInstance(TrimHomopolymerStartingSequence.class);
     private int readsCompletelyTrimmed = 0;
 
@@ -107,7 +108,7 @@ private void maybeClip(final SAMRecord r) {
             if (trimPosition == readBases.length) {
                 // if the entire read is a homopolymer run, set all qualities to Q3
                 byte[] value = new byte[readBases.length];
-                Arrays.fill(value, (byte) 3);
+                Arrays.fill(value, FULL_TRIM_QUALITY_SCORE);
                 r.setBaseQualities(value);
                 this.readsCompletelyTrimmed++;
             } else {

diff --git a/src/tests/java/org/broadinstitute/dropseqrna/readtrimming/ClipReadsTest.java b/src/tests/java/org/broadinstitute/dropseqrna/readtrimming/ClipReadsTest.java
@@ -46,7 +46,6 @@ public void testClipReads() {
         final ClipReads clp = new ClipReads();
         clp.INPUT = PAIRED_INPUT;
         clp.OUTPUT = TestUtils.getTempReportFile("ClipReadsTest.", ".sam");
-        clp.OUTPUT.deleteOnExit();
         clp.TMP_DIR = Collections.singletonList(tempDir);
         clp.BASE_RANGE = "1-16:17-28";
         clp.WHICH_READ = Collections.singletonList(AbstractTrimmerClp.FIRST_OF_PAIR);

diff --git a/.../java/org/broadinstitute/dropseqrna/readtrimming/TrimHomopolymerStartingSequenceTest.java b/.../java/org/broadinstitute/dropseqrna/readtrimming/TrimHomopolymerStartingSequenceTest.java
@@ -0,0 +1,91 @@
+/*
+ * MIT License
+ *
+ * Copyright 2025 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package org.broadinstitute.dropseqrna.readtrimming;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SAMRecordIterator;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.util.CloserUtil;
+import org.broadinstitute.dropseqrna.utils.TestUtils;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+
+public class TrimHomopolymerStartingSequenceTest {
+    private static final File TESTDATA_DIR = new File("testdata/org/broadinstitute/dropseq/readtrimming");
+    private static final File INPUT = new File(TESTDATA_DIR, "prePolyTTrim.paired.sam");
+
+    @Test
+    public void testBasic() {
+        final File tempDir = TestUtils.createTempDirectory("TrimHomopolymerStartingSequenceTest.");
+        final TrimHomopolymerStartingSequence clp = new TrimHomopolymerStartingSequence();
+        clp.INPUT = INPUT;
+        clp.OUTPUT = TestUtils.getTempReportFile("TrimHomopolymerStartingSequenceTest.", ".sam");
+        clp.WHICH_READ = Collections.singletonList(AbstractTrimmerClp.FIRST_OF_PAIR);
+        clp.TMP_DIR = Collections.singletonList(tempDir);
+        Assert.assertEquals(clp.doWork(), 0);
+
+        final SamReader inputReader = SamReaderFactory.makeDefault().open(clp.INPUT);
+        final SamReader actualReader = SamReaderFactory.makeDefault().open(clp.OUTPUT);
+        final SAMRecordIterator inputIterator = inputReader.iterator();
+        final SAMRecordIterator actualIterator = actualReader.iterator();
+        while (inputIterator.hasNext() && actualIterator.hasNext()) {
+            final SAMRecord inputRecord = inputIterator.next();
+            final SAMRecord actualRecord = actualIterator.next();
+            final String readName = actualRecord.getReadName();
+            Assert.assertEquals(readName, inputRecord.getReadName());
+            Assert.assertEquals(actualRecord.getFirstOfPairFlag(), inputRecord.getFirstOfPairFlag(), readName);
+            if (actualRecord.getFirstOfPairFlag()) {
+                final String[] readNameFields = readName.split(":");
+                if (readNameFields[0].equals("trimmed")) {
+                    final int trimLength = Integer.parseInt(readNameFields[1]);
+                    final String inputRead = inputRecord.getReadString().substring(trimLength);
+                    Assert.assertEquals(actualRecord.getReadString(), inputRead, readName);
+                    final String inputQual = inputRecord.getBaseQualityString().substring(trimLength);
+                    Assert.assertEquals(actualRecord.getBaseQualityString(), inputQual, readName);
+                } else if (readNameFields[0].equals("notrim")) {
+                    Assert.assertEquals(actualRecord, inputRecord);
+                } else if (readNameFields[0].equals("fulltrim")) {
+                    Assert.assertEquals(actualRecord.getReadString(), inputRecord.getReadString(), readName);
+                    byte[] expectedQuals = new byte[inputRecord.getReadLength()];
+                    Arrays.fill(expectedQuals, TrimHomopolymerStartingSequence.FULL_TRIM_QUALITY_SCORE);
+                    Assert.assertEquals(actualRecord.getBaseQualities(), expectedQuals, readName);
+                } else {
+                    Assert.fail("Unexpected read name: " + readName);
+                }
+            } else {
+                Assert.assertEquals(actualRecord, inputRecord);
+            }
+        }
+        Assert.assertFalse(inputIterator.hasNext());
+        Assert.assertFalse(actualIterator.hasNext());
+        CloserUtil.close(inputReader);
+        CloserUtil.close(actualReader);
+
+    }
+}
diff --git a/testdata/org/broadinstitute/dropseq/readtrimming/paired_end.28_technical.sam b/testdata/org/broadinstitute/dropseq/readtrimming/paired_end.28_technical.sam
@@ -1,8 +1,8 @@
 @HD	VN:1.6	GO:none	SO:queryname
-@RG	ID:A	SM:v29_10X-GEMX-3P_ic_rxn1	LB:v29_10X-GEMX-3P_ic_rxn1	PL:ILLUMINA	PU:22FKMMLT4.ACCAGACAAC.CCTAGTTCCT.1	CN:BI
-LH00453:184:22FKMMLT4:1:1101:10031:9853	77	*	0	0	*	*	0	0	ACCGGCTGTGAGACTACGCTGCGCAGCCTTGTTTTTTTTTTTTTTTTTTTTTCTGACCGTCTTCGAACCTCCCCCCTTCGTTCTTGCTTAATGCCAACATTCTTCGCAAATGCTTTCTATCTTATCCTTCTTTTACCCACCCAAAAACCT	-I9II9IIIIII9IIIIIII9IIIIII-9-------9I9999999I9I99-----99--9-99--99---------99--9--99--99-9999-99-9---99--99999-999---------99I--99---999---9---9----9	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:10031:9853	141	*	0	0	*	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	I--I----99II9I9I-I-9--I9I99999-I--99I----9-99------------9-99-9---9--99--9999-99-9-99----999-9--999--9-9999-9--999999-I99-I9-9I99I99---9-9999999-9999-	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A	XM:Z:CGCTGCGCAGCC
-LH00453:184:22FKMMLT4:1:1101:31945:11394	77	*	0	0	*	*	0	0	ATGCTAGTCACCCTGCTCTGCACTAGACTTTTTTTTTTTTTTTTTTTTTTGTAGTCACCAAAACTGTGAGGGGAGAAACCCCAAGCTCTCCCGCAAACCTCTCTCTCTCGTCACAACTATGTCTATTCCCCTTAACTTTTTCAAACAACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---9--9I-I99I9----99I99--99I9---99-99-99--9-9-9--9-----9I--------9-9-9---9-----9------9------9------	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:31945:11394	141	*	0	0	*	*	0	0	AGAATGAAGGCAATCAATATTTTTCACTTGCTTCTCCACTAAGTTTGTTATTGCACCCATTATTCAAACTTTCAAATTCCTGGTTGAAAAAATGCTCATCTTCAAAATTTACTATTAACAGCCACAATTGTCACCATATATATATATTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A	XM:Z:TCTGCACTAGAC
-LH00453:184:22FKMMLT4:1:1101:6236:13425	77	*	0	0	*	*	0	0	CTGTCATTCAGGAACGTGTGTGCCCAGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGACCAAGAAACCCCCCACCCAACAAAAAAAAACCAACACCCACAAACACTTTTCCGCTTTAAAACACCCACAACAAAAAATTTTTTTCCCAAG	IIIII9IIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-I--I9-99I-9I-I-9---I-I9--I9I-9I9---99-9-9---999II--9I9-9---9-9---------99--9--I9--9-9---9-----	XC:Z:CTGTCATTCAGGAACG	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:6236:13425	141	*	0	0	*	*	0	0	CAATGGTGCCTGTCCAGATTTTCTGACAGTCACCTCAGGAAATTGACACAGACACGCTGTGATCCTGGTTTCTGTACAGTTACTTTGTGTGTTACTCAGCACCTGGGCTGTTAAGGGTATTATCAAGCGTGAAAAAATAAAGACAAAAAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A	XM:Z:TGTGTGCCCAGC
+@RG	ID:A	SM:rxn1	LB:rxn1	PL:ILLUMINA	PU:123456789.ACCAGACAAC.CCTAGTTCCT.1	CN:BI
+LH00453:184:123456789:1:1101:10031:9853	77	*	0	0	*	*	0	0	ACCGGCTGTGAGACTACGCTGCGCAGCCTTGTTTTTTTTTTTTTTTTTTTTTCTGACCGTCTTCGAACCTCCCCCCTTCGTTCTTGCTTAATGCCAACATTCTTCGCAAATGCTTTCTATCTTATCCTTCTTTTACCCACCCAAAAACCT	-I9II9IIIIII9IIIIIII9IIIIII-9-------9I9999999I9I99-----99--9-99--99---------99--9--99--99-9999-99-9---99--99999-999---------99I--99---999---9---9----9	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A
+LH00453:184:123456789:1:1101:10031:9853	141	*	0	0	*	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	I--I----99II9I9I-I-9--I9I99999-I--99I----9-99------------9-99-9---9--99--9999-99-9-99----999-9--999--9-9999-9--999999-I99-I9-9I99I99---9-9999999-9999-	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A	XM:Z:CGCTGCGCAGCC
+LH00453:184:123456789:1:1101:31945:11394	77	*	0	0	*	*	0	0	ATGCTAGTCACCCTGCTCTGCACTAGACTTTTTTTTTTTTTTTTTTTTTTGTAGTCACCAAAACTGTGAGGGGAGAAACCCCAAGCTCTCCCGCAAACCTCTCTCTCTCGTCACAACTATGTCTATTCCCCTTAACTTTTTCAAACAACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---9--9I-I99I9----99I99--99I9---99-99-99--9-9-9--9-----9I--------9-9-9---9-----9------9------9------	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A
+LH00453:184:123456789:1:1101:31945:11394	141	*	0	0	*	*	0	0	AGAATGAAGGCAATCAATATTTTTCACTTGCTTCTCCACTAAGTTTGTTATTGCACCCATTATTCAAACTTTCAAATTCCTGGTTGAAAAAATGCTCATCTTCAAAATTTACTATTAACAGCCACAATTGTCACCATATATATATATTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A	XM:Z:TCTGCACTAGAC
+LH00453:184:123456789:1:1101:6236:13425	77	*	0	0	*	*	0	0	CTGTCATTCAGGAACGTGTGTGCCCAGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGACCAAGAAACCCCCCACCCAACAAAAAAAAACCAACACCCACAAACACTTTTCCGCTTTAAAACACCCACAACAAAAAATTTTTTTCCCAAG	IIIII9IIIIII-IIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIII-I--I9-99I-9I-I-9---I-I9--I9I-9I9---99-9-9---999II--9I9-9---9-9---------99--9--I9--9-9---9-----	XC:Z:CTGTCATTCAGGAACG	RG:Z:A
+LH00453:184:123456789:1:1101:6236:13425	141	*	0	0	*	*	0	0	CAATGGTGCCTGTCCAGATTTTCTGACAGTCACCTCAGGAAATTGACACAGACACGCTGTGATCCTGGTTTCTGTACAGTTACTTTGTGTGTTACTCAGCACCTGGGCTGTTAAGGGTATTATCAAGCGTGAAAAAATAAAGACAAAAAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A	XM:Z:TGTGTGCCCAGC
diff --git a/testdata/org/broadinstitute/dropseq/readtrimming/paired_end.28_technical.short_read.sam b/testdata/org/broadinstitute/dropseq/readtrimming/paired_end.28_technical.short_read.sam
@@ -1,8 +1,8 @@
 @HD	VN:1.6	GO:none	SO:queryname
-@RG	ID:A	SM:v29_10X-GEMX-3P_ic_rxn1	LB:v29_10X-GEMX-3P_ic_rxn1	PL:ILLUMINA	PU:22FKMMLT4.ACCAGACAAC.CCTAGTTCCT.1	CN:BI
-LH00453:184:22FKMMLT4:1:1101:10031:9853	77	*	0	0	*	*	0	0	ACCGGCTGTGAGACTACGCTGCGCAGCCT	-I9II9IIIIII9IIIIIII9IIIIII-9	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:10031:9853	141	*	0	0	*	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	I--I----99II9I9I-I-9--I9I99999-I--99I----9-99------------9-99-9---9--99--9999-99-9-99----999-9--999--9-9999-9--999999-I99-I9-9I99I99---9-9999999-9999-	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A	XM:Z:CGCTGCGCAGCC
-LH00453:184:22FKMMLT4:1:1101:31945:11394	77	*	0	0	*	*	0	0	ATGCTAGTCACCCTGCTCTGCACTAGACTTTTTTTTTTTTTTTTTTTTTTGTAGTCACCAAAACTGTGAGGGGAGAAACCCCAAGCTCTCCCGCAAACCTCTCTCTCTCGTCACAACTATGTCTATTCCCCTTAACTTTTTCAAACAACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---9--9I-I99I9----99I99--99I9---99-99-99--9-9-9--9-----9I--------9-9-9---9-----9------9------9------	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:31945:11394	141	*	0	0	*	*	0	0	AGAATGAAGGCAATCAATATTTTTCACTTGCTTCTCCACTAAGTTTGTTATTGCACCCATTATTCAAACTTTCAAATTCCTGGTTGAAAAAATGCTCATCTTCAAAATTTACTATTAACAGCCACAATTGTCACCATATATATATATTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A	XM:Z:TCTGCACTAGAC
-LH00453:184:22FKMMLT4:1:1101:6236:13425	77	*	0	0	*	*	0	0	CTGTCATTCAGGAACGTGTG	IIIII9IIIIII-IIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A
-LH00453:184:22FKMMLT4:1:1101:6236:13425	141	*	0	0	*	*	0	0	CAATGGTGCCTGTCCAGATTTTCTGACAGTCACCTCAGGAAATTGACACAGACACGCTGTGATCCTGGTTTCTGTACAGTTACTTTGTGTGTTACTCAGCACCTGGGCTGTTAAGGGTATTATCAAGCGTGAAAAAATAAAGACAAAAAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A	XM:Z:TGTGTGCCCAGC
+@RG	ID:A	SM:rxn1	LB:rxn1	PL:ILLUMINA	PU:123456789.ACCAGACAAC.CCTAGTTCCT.1	CN:BI
+LH00453:184:123456789:1:1101:10031:9853	77	*	0	0	*	*	0	0	ACCGGCTGTGAGACTACGCTGCGCAGCCT	-I9II9IIIIII9IIIIIII9IIIIII-9	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A
+LH00453:184:123456789:1:1101:10031:9853	141	*	0	0	*	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	I--I----99II9I9I-I-9--I9I99999-I--99I----9-99------------9-99-9---9--99--9999-99-9-99----999-9--999--9-9999-9--999999-I99-I9-9I99I99---9-9999999-9999-	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A	XM:Z:CGCTGCGCAGCC
+LH00453:184:123456789:1:1101:31945:11394	77	*	0	0	*	*	0	0	ATGCTAGTCACCCTGCTCTGCACTAGACTTTTTTTTTTTTTTTTTTTTTTGTAGTCACCAAAACTGTGAGGGGAGAAACCCCAAGCTCTCCCGCAAACCTCTCTCTCTCGTCACAACTATGTCTATTCCCCTTAACTTTTTCAAACAACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---9--9I-I99I9----99I99--99I9---99-99-99--9-9-9--9-----9I--------9-9-9---9-----9------9------9------	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A
+LH00453:184:123456789:1:1101:31945:11394	141	*	0	0	*	*	0	0	AGAATGAAGGCAATCAATATTTTTCACTTGCTTCTCCACTAAGTTTGTTATTGCACCCATTATTCAAACTTTCAAATTCCTGGTTGAAAAAATGCTCATCTTCAAAATTTACTATTAACAGCCACAATTGTCACCATATATATATATTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:ATGCTAGTCACCCTGC	RG:Z:A	XM:Z:TCTGCACTAGAC
+LH00453:184:123456789:1:1101:6236:13425	77	*	0	0	*	*	0	0	CTGTCATTCAGGAACGTGTG	IIIII9IIIIII-IIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A
+LH00453:184:123456789:1:1101:6236:13425	141	*	0	0	*	*	0	0	CAATGGTGCCTGTCCAGATTTTCTGACAGTCACCTCAGGAAATTGACACAGACACGCTGTGATCCTGGTTTCTGTACAGTTACTTTGTGTGTTACTCAGCACCTGGGCTGTTAAGGGTATTATCAAGCGTGAAAAAATAAAGACAAAAAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:CTGTCATTCAGGAACG	RG:Z:A	XM:Z:TGTGTGCCCAGC
diff --git a/testdata/org/broadinstitute/dropseq/readtrimming/prePolyTTrim.paired.sam b/testdata/org/broadinstitute/dropseq/readtrimming/prePolyTTrim.paired.sam
@@ -0,0 +1,9 @@
+@HD	VN:1.6	GO:none	SO:queryname
+@RG	ID:A	SM:rxn1	LB:rxn1	PL:ILLUMINA	PU:123456789.ACCAGACAAC.CCTAGTTCCT.1	CN:BI
+@CO	tests ordered by read name
+fulltrim	77	*	0	0	*	*	0	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII999999-999999999--99999-99I999IIII9	XC:Z:CGAATAGGTCTTGAGT	RG:Z:A
+fulltrim	141	*	0	0	*	*	0	0	TCTGGAACATGGATTTGTGTTCACCTTAAATGTGAAAATAAATCCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:CGAATAGGTCTTGAGT	RG:Z:A	ZL:i:104	XM:Z:ACGATTTACAGC	ZP:i:47
+notrim:tooshort	77	*	0	0	*	*	0	0	TCCACATCTTCCGGAAAAAATCCAGGTCTTCCAGCCAATATATGTCTTCCTGAAGATCCACGTCTTCCAGAAAATCCATGTCTTCCAGAAAATCCATGTCTTCCAGTAACCTCCCAGTCTTC	IIIIIIIIIIIIIIIIIIIIIIIIIII-I9I9II99I--II9999-99-9999999I9-99I9-99-99I99-I---999I--9--99-999-9I-999I-9999I-9II99-9I9I999II	XC:Z:GCTAGTCAGTGCCTGG	RG:Z:A
+notrim:tooshort	141	*	0	0	*	*	0	0	AAGACACAAGTAGGCTGGAAGACATTAATTTGATGGAAGACATGGCTTTGTTGGAAGACGTGGATTTGCTGGAAGACACGGATTTCCTGGAAGACCTGGATTTTTCGGAAGCTATGGATTTGAGGGAAGACAAGGATTTTCTGGAAGACA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII	XC:Z:GCTAGTCAGTGCCTGG	RG:Z:A	XM:Z:TCTTCCAGTCAA
+trimmed:24	77	*	0	0	*	*	0	0	TTGTTTTTTTTTTTTTTTTTTTTTCTGACCGTCTTCGAACCTCCCCCCTTCGTTCTTGCTTAATGCCAACATTCTTCGCAAATGCTTTCTATCTTATCCTTCTTTTACCCACCCAAAAACCT	9-------9I9999999I9I99-----99--9-99--99---------99--9--99--99-9999-99-9---99--99999-999---------99I--99---999---9---9----9	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A
+trimmed:24	141	*	0	0	*	*	0	0	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	I--I----99II9I9I-I-9--I9I99999-I--99I----9-99------------9-99-9---9--99--9999-99-9-99----999-9--999--9-9999-9--999999-I99-I9-9I99I99---9-9999999-9999-	XC:Z:ACCGGCTGTGAGACTA	RG:Z:A	XM:Z:CGCTGCGCAGCC