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tests for ReplaceSamHeader (some disabled due to picard bug broadinst…
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…itute/picard#284)
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@akiezun
akiezun committed Sep 16, 2015
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97 changes: 97 additions & 0 deletions .../java/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeaderIntegrationTest.java
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package org.broadinstitute.hellbender.tools.picard.sam;

import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.IntegrationTestSpec;
import org.broadinstitute.hellbender.utils.read.SamAssertionUtils;
import org.broadinstitute.hellbender.utils.test.BaseTest;
import org.testng.annotations.Test;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

public final class ReplaceSamHeaderIntegrationTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = getTestDataDir();
private static final File BAM_FILE1 = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/first10.bam");
private static final File SAM_FILE1 = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/first10.sam");
private static final File BAM_FILE2 = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/file2.bam");
private static final File SAM_FILE2 = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/file2.sam");
private static final File SAM_FILE2_QUERYSORT = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/file2NameSorted.sam");

public String getTestedClassName() {
return ReplaceSamHeader.class.getSimpleName();
}

@Test
public void testSamSamSam() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".sam");
runIt(SAM_FILE1, SAM_FILE2, outputFile);
final File expectedOut = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/samSam.sam");

//TODO fails due to picard bug https://github.com/broadinstitute/picard/issues/284
// SamAssertionUtils.assertSamsEqual(expectedOut, outputFile, ValidationStringency.SILENT);

//using text comparison
IntegrationTestSpec.assertEqualTextFiles(expectedOut, outputFile);
}

@Test(expectedExceptions = UserException.class)
public void testSamSamSam_clashingSort() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".sam");
runIt(SAM_FILE1, SAM_FILE2_QUERYSORT, outputFile);
}

@Test(enabled = false) //disabled due to picard bug https://github.com/broadinstitute/picard/issues/284
public void testSamSamBam() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".bam");
runIt(SAM_FILE1, SAM_FILE2, outputFile);
final File expectedOut = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/samSam.bam");

SamAssertionUtils.assertSamsEqual(expectedOut, outputFile, ValidationStringency.SILENT);
}

@Test
public void testSamBamSam() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".sam");
runIt(SAM_FILE1, BAM_FILE2, outputFile);
final File expectedOut = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/samBam.sam");

//TODO fails due to picard bug https://github.com/broadinstitute/picard/issues/284
// SamAssertionUtils.assertSamsEqual(expectedOut, outputFile, ValidationStringency.SILENT);

//using text comparison
IntegrationTestSpec.assertEqualTextFiles(expectedOut, outputFile);
}

@Test(enabled = false) //disabled due to picard bug https://github.com/broadinstitute/picard/issues/284
public void testSamBamBam() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".bam");
runIt(SAM_FILE1, BAM_FILE2, outputFile);
final File expectedOut = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/samBam.bam");

SamAssertionUtils.assertSamsEqual(expectedOut, outputFile, ValidationStringency.SILENT);
}

@Test(enabled = false) //disabled due to picard bug https://github.com/broadinstitute/picard/issues/284
public void testBamBamBam() throws Exception {
final File outputFile = BaseTest.createTempFile("ReplaceSamHeader.testBasic", ".bam");
runIt(BAM_FILE1, BAM_FILE2, outputFile);
final File expectedOut = new File(TEST_DATA_DIR, "picard/sam/ReplaceSamHeader/bamBam.bam");

SamAssertionUtils.assertSamsEqual(expectedOut, outputFile, ValidationStringency.SILENT);
}

private void runIt(final File inputFile, final File inputHeaderFile, final File outputFile) {
final List<String> args = new ArrayList<>(Arrays.asList(
"--INPUT", inputFile.getAbsolutePath(),
"--HEADER", inputHeaderFile.getAbsolutePath(),
"--OUTPUT", outputFile.getAbsolutePath()
)
);
runCommandLine(args);
}

}
2 changes: 1 addition & 1 deletion src/test/java/org/broadinstitute/hellbender/utils/read/SamAssertionUtils.java
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Expand Up @@ -30,7 +30,7 @@ public static void assertSamsEqual(final File sam1, final File sam2, final Valid
final SamReader reader2 = getReader(sam2, validationStringency, reference)) {
final SamComparison comparison = new SamComparison(reader1, reader2);
final boolean equal = comparison.areEqual();
Assert.assertTrue(equal, "SAM file output differs from expected output");
Assert.assertTrue(equal, "SAM file " + sam1.getPath() + " differs from expected output:" + sam2.getPath());
}
}

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Binary file added src/test/resources/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/file2.bam
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30 changes: 30 additions & 0 deletions src/test/resources/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/file2.sam
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@HD VN:1.5 SO:coordinate
@SQ SN:chr1 LN:101
@SQ SN:chr2 LN:101
@SQ SN:chr3 LN:101
@SQ SN:chr4 LN:101
@SQ SN:chr5 LN:101
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:202
@SQ SN:chr8 LN:202
@SQ SN:20 LN:20000000
@RG ID:0 SM:Hi,Momma! LB:whatever PU:me PL:ILLUMINA
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 XN:i:1
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 XN:i:1
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
30 changes: 30 additions & 0 deletions ...urces/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/file2NameSorted.sam
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@HD VN:1.5 SO:queryname
@SQ SN:chr1 LN:101
@SQ SN:chr2 LN:101
@SQ SN:chr3 LN:101
@SQ SN:chr4 LN:101
@SQ SN:chr5 LN:101
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:202
@SQ SN:chr8 LN:202
@SQ SN:20 LN:20000000
@RG ID:0 SM:Hi,Momma! LB:whatever PU:me PL:ILLUMINA
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
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
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
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
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
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
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
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 XN:i:1
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
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
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
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
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
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
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 XN:i:1
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
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
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
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
Binary file added ...est/resources/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/first10.bam
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17 changes: 17 additions & 0 deletions ...est/resources/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/first10.sam
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@@ -0,0 +1,17 @@
@HD VN:1.5 GO:none SO:coordinate
@SQ SN:20 LN:20000000
@RG ID:1 PL:illumina PU:unit1 LB:lib1 SM:20
@RG ID:2 PL:illumina PU:unit1 LB:lib1 SM:20
@PG ID:MarkDuplicates PN:MarkDuplicates VN:1.775(f12398c918921ad38c0b8bcc5e68cf1c41738541_1412863936) CL:picard.sam.markduplicates.MarkDuplicates INPUT=[snippet.bam] OUTPUT=dedupped.bam METRICS_FILE=metrics.txt MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
@CO SLC16A1
@CO SLC16A1
20FUKAAXX100202:6:27:4968:125377 97 20 9999902 27 95M2I4M = 10000376 575 TGTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTT DEDEFGGHFFFGHEHFGEFGGGGGEGFGGGGGFFFGGGCBHGFGEHFHGGGFGGGGGFFGGGGHEGHGGGGGHGHGGGGHGGGGGGHGGGEGHFHEHGFGG PG:Z:MarkDuplicates RG:Z:1 NM:i:2 AS:i:95 XS:i:76
20FUKAAXX100202:6:27:4968:125377 97 20 9999902 27 95M2I4M = 10000376 575 TGTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTT DEDEFGGHFFFGHEHFGEFGGGGGEGFGGGGGFFFGGGCBHGFGEHFHGGGFGGGGGFFGGGGHEGHGGGGGHGHGGGGHGGGGGGHGGGEGHFHEHGFGG PG:Z:MarkDuplicates RG:Z:2 NM:i:2 AS:i:95 XS:i:76
20FUKAAXX100202:6:27:4986:125375 1153 20 9999902 60 95M2I4M = 18041280 8041379 TGTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTT DEDEFGGHFFFGHEHFGEFGGGGGEGFGGGGGFFFGGGCBHGFGEHFHGGGFGGGGGFFGGGGHEGHGGGGGHGHGGGGHGGGGGGHGGGEGHFHEHGFGG PG:Z:MarkDuplicates RG:Z:1 NM:i:2 AS:i:95 XS:i:22
20FUKAAXX100202:6:27:4986:125375 1153 20 9999902 60 95M2I4M = 18041280 8041379 TGTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTT DEDEFGGHFFFGHEHFGEFGGGGGEGFGGGGGFFFGGGCBHGFGEHFHGGGFGGGGGFFGGGGHEGHGGGGGHGHGGGGHGGGGGGHGGGEGHFHEHGFGG PG:Z:MarkDuplicates RG:Z:2 NM:i:2 AS:i:95 XS:i:22
20FUKAAXX100202:8:65:6304:46134 113 20 9999903 60 94M2I5M = 15494113 5494213 GTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTT EIGGFGEFHGGGHHGGEGFGHGDHEGCHHF?BHGGFHHGHEGFGHGHGHEGHFGHGGGGHGFAGGFGFGGGGGGGGGGHFGGFGFHEFBFFFFFFGDGFFE PG:Z:MarkDuplicates RG:Z:1 NM:i:2 AS:i:94 XS:i:23
20FUKAAXX100202:8:65:6304:46134 113 20 9999903 60 94M2I5M = 15494113 5494213 GTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTT EIGGFGEFHGGGHHGGEGFGHGDHEGCHHF?BHGGFHHGHEGFGHGHGHEGHFGHGGGGHGFAGGFGFGGGGGGGGGGHFGGFGFHEFBFFFFFFGDGFFE PG:Z:MarkDuplicates RG:Z:2 NM:i:2 AS:i:94 XS:i:23
20GAVAAXX100126:1:7:1484:95625 177 20 9999903 60 94M2I5M = 18941082 8941182 GTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTT :ECC>>4DHFHFFHGCGFGGHFEHEGGIHGCDIGGIIHGHEGFGEGIGHEGHDGHHGFGHHFCGFGGGGHBHGGGHGFHGFHFFFHEGFFFFFFFGDBFFD PG:Z:MarkDuplicates RG:Z:1 NM:i:2 AS:i:94 XS:i:23
20GAVAAXX100126:1:7:1484:95625 177 20 9999903 60 94M2I5M = 18941082 8941182 GTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTT :ECC>>4DHFHFFHGCGFGGHFEHEGGIHGCDIGGIIHGHEGFGEGIGHEGHDGHHGFGHHFCGFGGGGHBHGGGHGFHGFHFFFHEGFFFFFFFGDBFFD PG:Z:MarkDuplicates RG:Z:2 NM:i:2 AS:i:94 XS:i:23
20FUKAAXX100202:5:62:8987:1929 97 20 9999905 60 92M2I7M = 13584266 3584462 TAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTTGT ADEECCDDFGDGFGDFGGFGGDGFGGFGGFGFGGFDCHGFGEHFHGGGGGGHGGFFHGGGHEGHGGGGFHFHGGGGHGGGGGGGGGGEGHEHEHEFFFFGF PG:Z:MarkDuplicates RG:Z:1 NM:i:2 AS:i:92 XS:i:24
20FUKAAXX100202:5:62:8987:1929 97 20 9999905 60 92M2I7M = 13584266 3584462 TAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCCATTGACCTATATCTCTATCCTTATGCCAGTACCACACTGTTTTGT ADEECCDDFGDGFGDFGGFGGDGFGGFGGFGFGGFDCHGFGEHFHGGGGGGHGGFFHGGGHEGHGGGGFHFHGGGGHGGGGGGGGGGEGHEHEHEFFFFGF PG:Z:MarkDuplicates RG:Z:2 NM:i:2 AS:i:92 XS:i:24
Binary file added ...test/resources/org/broadinstitute/hellbender/tools/picard/sam/ReplaceSamHeader/samBam.bam
View file
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