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wbrockmanwbrockman
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Merge pull request #45 from lbergelson/lb_ReadConverterFix
Fixing a few bugs in ReadConverter and adding a new test for Sam -> Read -> Sam conversion.
2 parents d8b04b5 + 0a20aa7 commit 48b0bad

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4 files changed

+72
-20
lines changed

4 files changed

+72
-20
lines changed

‎pom.xml‎

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@@ -207,6 +207,11 @@
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.google.cloud.genomics</groupId>
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<artifactId>gatk-tools-java</artifactId>
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<version>1.0</version>
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</dependency>
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</dependencies>
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<profiles>

‎src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReadConverter.java‎

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@@ -15,6 +15,7 @@
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*/
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package com.google.cloud.genomics.dataflow.readers.bam;
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import com.google.api.client.util.Maps;
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import com.google.api.services.genomics.model.CigarUnit;
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import com.google.api.services.genomics.model.LinearAlignment;
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import com.google.api.services.genomics.model.Position;
@@ -23,15 +24,12 @@
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import com.google.common.collect.BiMap;
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import com.google.common.collect.HashBiMap;
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import com.google.common.collect.Lists;
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import htsjdk.samtools.CigarElement;
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import htsjdk.samtools.CigarOperator;
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import htsjdk.samtools.SAMException;
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import htsjdk.samtools.SAMRecord;
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import htsjdk.samtools.*;
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import htsjdk.samtools.util.SequenceUtil;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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/**
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* Converts SAMRecords to Reads.
@@ -62,7 +60,7 @@ public static final Read makeRead(final SAMRecord record) {
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read.setId(record.getReadName()); // TODO: make more unique
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read.setFragmentName(record.getReadName());
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read.setReadGroupId(getAttr(record, "RG"));
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read.setNumberReads(record.getReadPairedFlag() ? 1 : 2);
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read.setNumberReads(record.getReadPairedFlag() ? 2 : 1);
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read.setProperPlacement(record.getReadPairedFlag() && record.getProperPairFlag());
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if (!record.getReadUnmappedFlag() && record.getAlignmentStart() > 0) {
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LinearAlignment alignment = new LinearAlignment();
@@ -97,7 +95,7 @@ public CigarUnit apply(CigarElement c) {
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read.setAlignment(alignment);
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}
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read.setDuplicateFragment(record.getDuplicateReadFlag());
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read.setFragmentLength(record.getReadLength());
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read.setFragmentLength(record.getInferredInsertSize());
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if (record.getReadPairedFlag()) {
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if (record.getFirstOfPairFlag()) {
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read.setReadNumber(0);
@@ -126,6 +124,12 @@ public CigarUnit apply(CigarElement c) {
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read.setAlignedQuality(readBaseQualities);
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}
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Map<String, List<String>> attributes = Maps.newHashMap();
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for( SAMRecord.SAMTagAndValue tagAndValue: record.getAttributes()) {
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attributes.put(tagAndValue.tag, Lists.newArrayList(tagAndValue.value.toString()));
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}
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read.setInfo(attributes);
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return read;
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}
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‎src/test/java/com/google/cloud/genomics/dataflow/readers/bam/ReadConverterTest.java‎

Lines changed: 27 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,19 @@
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package com.google.cloud.genomics.dataflow.readers.bam;
22

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import com.google.api.services.genomics.model.Read;
4-
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import static org.junit.Assert.assertEquals;
6-
import static org.junit.Assert.assertFalse;
7-
import static org.junit.Assert.assertThat;
8-
import static org.junit.Assert.assertTrue;
9-
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import java.util.Arrays;
11-
import java.util.Comparator;
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import java.util.List;
13-
14-
import org.junit.Before;
4+
import com.google.cloud.genomics.gatk.common.GenomicsConverter;
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import htsjdk.samtools.SAMFileHeader;
6+
import htsjdk.samtools.SAMRecord;
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import htsjdk.samtools.SamReader;
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import htsjdk.samtools.SamReaderFactory;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.junit.runners.JUnit4;
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import htsjdk.samtools.SAMRecord;
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import java.io.File;
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import java.io.IOException;
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import static org.junit.Assert.assertEquals;
2017

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@RunWith(JUnit4.class)
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public class ReadConverterTest {
@@ -41,5 +38,22 @@ public void testConversion() {
4138
assertEquals("chr20", read.getNextMatePosition().getReferenceName());
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assertEquals((Boolean)true, read.getNextMatePosition().getReverseStrand());
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}
44-
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@Test
43+
public void SamToReadToSamTest() throws IOException {
44+
String filePath = "src/test/resources/com/google/cloud/genomics/dataflow/readers/bam/conversion_test.sam";
45+
File samInput = new File(filePath);
46+
SamReader reads = SamReaderFactory.makeDefault().open(samInput);
47+
SAMFileHeader header = reads.getFileHeader();
48+
49+
int numReads = 0;
50+
for (SAMRecord sam : reads){
51+
Read read = ReadConverter.makeRead(sam);
52+
SAMRecord newSam = GenomicsConverter.makeSAMRecord(read, header );
53+
assertEquals(newSam.getSAMString(), sam.getSAMString());
54+
numReads++;
55+
}
56+
assertEquals(19, numReads);//sanity check to make sure we actually read the file
57+
}
58+
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}

‎src/test/resources/com/google/cloud/genomics/dataflow/readers/bam/conversion_test.sam‎

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@HD VN:1.0 SO:coordinate
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@SQ SN:chr1 LN:101
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@SQ SN:chr2 LN:101
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@SQ SN:chr3 LN:101
5+
@SQ SN:chr4 LN:101
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@SQ SN:chr5 LN:101
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@SQ SN:chr6 LN:101
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@SQ SN:chr7 LN:202
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@SQ SN:chr8 LN:202
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@RG ID:0 SM:Hi,Momma! LB:whatever PU:me PL:ILLUMINA
11+
SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 NN:Z:Hello
12+
SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 NN:Z:Goodbye
13+
SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0
14+
SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0
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SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0
16+
SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0
17+
SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
18+
SL-XAV:1:1:0:105#0/2 403 chr7 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0
19+
SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
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SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0
21+
SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0
22+
SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0
23+
SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0
24+
SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0
25+
SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0
26+
SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0
27+
SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0
28+
SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0
29+
SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0

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