Fixes LiftoverVCF for indels (again) #1469

yfarjoun · 2020-02-15T20:22:04Z

included getStop() from rev'ed htsJDK.
fixes (again) LiftoverVCF + Badly formed variant context at location chr1:899903; getEnd() #1258 which was still broken due to the call to "make()" in the presence of a mismatching "END" attribute and "getEnd()" result.
modified a test that is fixed by this commit (checked that it failing prior to the change)

Thanks to the several users who reported this is still a problem, and sorry for ignoring you for a year. @nh13, @kirannarta, and @duartemolha!

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- fixes (again) #1258 which was still broken due to the call to "make()" in the presence of a mismatching "END" attribute and "getEnd()" result.

pshapiro4broad

Java code looks ok; can't say I fully understand the fix or the test though.

nh13 · 2020-02-18T16:48:35Z

src/test/java/picard/util/LiftoverVcfTest.java

+    public void testLiftOverIndels(final LiftOver liftOver, final ReferenceSequence reference, final VariantContext source, final VariantContext result) {
+
+        final Interval target = liftOver.liftOver(new Interval(source.getContig(), source.getStart(), source.getEnd()), 1);
+


nh13 · 2020-02-18T16:56:27Z

@yfarjoun I am going to see if I can make a simple test case for #1280 and see if this fixes it.

nh13 · 2020-02-18T17:19:47Z

@yfarjoun this fix does not solve my issue: #1280. I have a single-variant test case in that PR.

yfarjoun · 2020-02-18T20:36:17Z

@nh13 while this PR was not intended to fix your other PR, I found the cause and I think I fixed it...care to test? (and review the PR while you're at it...) 😄

yfarjoun · 2020-02-18T20:38:15Z

@pshapiro4broad the problem was that the old code called "build()" on a builder that was in an improper state, the end of the variant was not at the same place where the END attribute was (for a non symbolic variant), and this didn't validate.

The changes to the tests simply adds the END attribute so that this problem is triggered, indeed the modified tests failed before I made the change.

- Symbolic alleles are now lifted over as well, by simply carrying them along.

yfarjoun · 2020-02-19T22:54:49Z

@nh13 you inspired me to make this work on symbolic alleles as well...and then I also figured out that I can simplify the code around the liftover that involves reverse-complementing....anyhow, no good deed will go unpunished....want to review this?

nh13 · 2020-02-19T23:15:37Z

@yfarjoun I can review if it helps. I won't be able to look at it until this weekend given my current workload. Is that allright?

yfarjoun · 2020-02-20T07:53:26Z

Fine with me. Thanks!

…

On Thu, Feb 20, 2020 at 1:15 AM Nils Homer ***@***.***> wrote: @yfarjoun <https://github.com/yfarjoun> I can review if it helps. I won't be able to look at it until this weekend given my current workload. Is that allright? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1469?email_source=notifications&email_token=AAU6JUSMAUFOAKLSJ7KVOGTRDW4RVA5CNFSM4KV37CV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKCSNY#issuecomment-588523831>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAU6JUREVBZEPQC4X56EFLDRDW4RVANCNFSM4KV37CVQ> .

chengdai · 2020-02-28T19:07:22Z

Any chance there has been an update to this? I'm encountering a similar error with the following genotype (test.b37.vcf.gz). For reference, I am trying to lift over genotypes from build 37 to build 38. I'm using the b37ToHg38 chain and GRCh38_full_analysis_set_plus_decoy_hla.fa found on the 1000 Genomes FTP

1       144609982       rs201830440     AATATATATATATAT A,<NON_REF>     788.73  .       DB;DP=28;ExcessHet=3.0103;MLEAC=1,1;MLEAF=0.5,0.5;RAW_MQ=68809;AC=1,1;AN=2      GT:AD:DP:GQ:PL:SB 1/2:0,19,0,0,0,0,0:19:2:824,41,194,783,0,780:0,0,9,10

The error message is:

[Fri Feb 28 19:05:05 UTC 2020] Executing as root@9823faf0b713 on Linux 4.14.154-128.181.amzn2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.22.0-SNAPSHOT
INFO    2020-02-28 19:05:05     LiftoverVcf     Loading up the target reference genome.
INFO    2020-02-28 19:05:15     LiftoverVcf     Lifting variants over and sorting (not yet writing the output file.)
[Fri Feb 28 19:05:15 UTC 2020] picard.vcf.LiftoverVcf done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=6722945024
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
        at picard.util.LiftoverUtils.lambda$leftAlignVariant$4(LiftoverUtils.java:379)
        at java.util.stream.Collectors.lambda$groupingBy$45(Collectors.java:907)
        at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
        at java.util.HashMap$ValueSpliterator.forEachRemaining(HashMap.java:1620)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
        at picard.util.LiftoverUtils.leftAlignVariant(LiftoverUtils.java:379)
        at picard.util.LiftoverUtils.reverseComplementVariantContext(LiftoverUtils.java:178)
        at picard.util.LiftoverUtils.liftVariant(LiftoverUtils.java:76)
        at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:426)
        at picard.cmdline.CommandLineProgram.instanc
[test.b37.vcf.gz](https://github.com/broadinstitute/picard/files/4268648/test.b37.vcf.gz)
eMain(CommandLineProgram.java:305)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

Thanks!

nh13 · 2020-02-28T20:09:51Z

Sorry, I'm extremely busy at work and haven't had time outside of work to look at this. Please do not wait on my review to hold this up, as I cannot commit to doing it in the next two weeks (work + vacation)

…ibute

pshapiro4broad

Looks OK to me, only some very minor formatting changes.

pshapiro4broad · 2020-02-20T18:16:16Z

src/main/java/picard/util/LiftoverUtils.java

+            return true;
+        }
+
+       return vc.getAlleles().stream().filter(a -> !a.isSymbolic()).filter(a -> !a.equals(Allele.SPAN_DEL)).


Not sure if the sun/oracle java code guidelines cover streaming operations yet, but I think it's more readable if each stream segment starts a new line:

return vc.getAlleles().stream() .filter(a -> !a.isSymbolic()) .filter(a -> !a.equals(Allele.SPAN_DEL)) .anyMatch(a -> a.length() != 1);

pshapiro4broad · 2020-04-03T14:40:27Z

src/main/java/picard/util/LiftoverUtils.java

@@ -365,7 +359,9 @@ protected static void leftAlignVariant(final VariantContextBuilder builder, fina

        // Put each allele into the alleleBasesMap unless it is a spanning deletion.
        // Spanning deletions are dealt with as a special case later in fixedAlleleMap.
-        alleles.stream().filter(a->!a.equals(Allele.SPAN_DEL)).forEach(a -> alleleBasesMap.put(a, a.getBases()));
+        alleles.stream()
+                .filter(a->!a.equals(Allele.SPAN_DEL)&&!a.isSymbolic())


whitespace

Suggested change

.filter(a->!a.equals(Allele.SPAN_DEL)&&!a.isSymbolic())

.filter(a -> !a.equals(Allele.SPAN_DEL) && !a.isSymbolic())

also, above you write filter(a -> !a.isSymbolic()).filter(a -> !a.equals(Allele.SPAN_DEL). The version with one call to filter() is probably clearer, either way I would use the same form in both places to be consistent.

pshapiro4broad · 2020-04-03T14:41:54Z

src/main/java/picard/util/LiftoverUtils.java

-
-        for (final Allele oldAllele : originalAlleles) {
-            alleles.add(LiftoverUtils.reverseComplement(oldAllele, target, refSeq, isIndel, addToStart));
+    private static boolean isIndelForLiftover(final VariantContext vc){


whitespace

Suggested change

private static boolean isIndelForLiftover(final VariantContext vc){

private static boolean isIndelForLiftover(final VariantContext vc) {

…ibute

- included getStop from rev'ed htsJDK.

1a2e5ee

- fixes (again) #1258 which was still broken due to the call to "make()" in the presence of a mismatching "END" attribute and "getEnd()" result.

yfarjoun requested a review from fleharty February 15, 2020 20:22

- typos

b9c6802

pshapiro4broad previously approved these changes Feb 18, 2020

View reviewed changes

nh13 reviewed Feb 18, 2020

View reviewed changes

- making Symbolic Alleles great again!

2366b46

yfarjoun dismissed pshapiro4broad’s stale review via 2366b46 February 18, 2020 20:27

nh13 mentioned this pull request Feb 18, 2020

Liftover gVCFs with indels #1280

Closed

Yossi Farjoun added 4 commits February 19, 2020 14:46

- WIP. problems with tests....

f93689d

- WIP. problems with tests....

828705b

- Greatly simplified liftover logic for indels.

34d6765

- Symbolic alleles are now lifted over as well, by simply carrying them along.

- cleanup

6f81b94

yfarjoun requested a review from nh13 March 25, 2020 19:30

Merge branch 'master' into yf_liftover_still_has_issues_with_END_attr…

cd95c01

…ibute

pshapiro4broad approved these changes Apr 3, 2020

View reviewed changes

Yossi Farjoun added 2 commits April 3, 2020 14:46

-whitespaces

f59b04e

Merge branch 'master' into yf_liftover_still_has_issues_with_END_attr…

6a1bdbe

…ibute

yfarjoun merged commit f20d6ec into master Apr 6, 2020

yfarjoun deleted the yf_liftover_still_has_issues_with_END_attribute branch April 6, 2020 18:14

Tintest mentioned this pull request Apr 7, 2020

LiftoverVCF doesn't seem to work with VCF from GATK4 Germline CNV caller #1495

Closed

1 task

karenfeng mentioned this pull request Jul 27, 2020

Variant Liftover exception projectglow/glow#261

Closed

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Fixes LiftoverVCF for indels (again) #1469

Fixes LiftoverVCF for indels (again) #1469

yfarjoun commented Feb 15, 2020 •

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pshapiro4broad Apr 3, 2020

		public void testLiftOverIndels(final LiftOver liftOver, final ReferenceSequence reference, final VariantContext source, final VariantContext result) {

		final Interval target = liftOver.liftOver(new Interval(source.getContig(), source.getStart(), source.getEnd()), 1);

	.filter(a->!a.equals(Allele.SPAN_DEL)&&!a.isSymbolic())
	.filter(a -> !a.equals(Allele.SPAN_DEL) && !a.isSymbolic())

	private static boolean isIndelForLiftover(final VariantContext vc){
	private static boolean isIndelForLiftover(final VariantContext vc) {

Fixes LiftoverVCF for indels (again) #1469

Fixes LiftoverVCF for indels (again) #1469

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