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equal treatment for supplementary alignments #137

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Merged
merged 3 commits into from
May 21, 2020
Merged

equal treatment for supplementary alignments #137

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e1e4fd8
equal treatment for supplementary alignments
tedsharpe May 18, 2020
ef4abc6
added test
tedsharpe May 20, 2020
c6695c1
revert version bump
tedsharpe May 21, 2020
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2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

<groupId>org.disq-bio</groupId>
<artifactId>disq</artifactId>
<version>0.3.6-SNAPSHOT</version>
<version>0.3.7-SNAPSHOT</version>
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I think you accidentally included the snapshot version change here. Could you revert that?

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Sure, but I thought we'd want to bump the version with this PR.

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It gets bumped automatically as part of the release process. If we bump it manually we'll end up skipping a version.

<name>Disq</name>
<description>A library for manipulating bioinformatics sequencing formats in Apache Spark.</description>
<url>https://github.com/disq-bio/disq</url>
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7 changes: 5 additions & 2 deletions src/main/java/org/disq_bio/disq/impl/formats/bam/BamRecordGuesser.java
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Expand Up @@ -173,8 +173,11 @@ private Result checkRecordStartInternal(long vPos) throws IOException {

boolean mapped = SAMFlag.READ_UNMAPPED.isUnset(flags);
boolean secondary = SAMFlag.SECONDARY_ALIGNMENT.isSet(flags);
if (mapped && ((seqLength == 0 && !secondary) || numCigarOps == 0)) {
// Non-empty cigar/seq in mapped reads, except secondary alignments can have '*' seq
boolean supplementary = SAMFlag.SUPPLEMENTARY_ALIGNMENT.isSet(flags);
boolean primaryLine = !secondary && !supplementary;
if (mapped && ((seqLength == 0 && primaryLine) || numCigarOps == 0)) {
// Non-empty cigar/seq in mapped reads
// except secondary and supplementary alignments can have '*' seq
return NO_START;
}

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Binary file modified src/test/resources/zero-length-secondary-alignment.bam
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