fix tabix index generation #7858
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crude, but effective |
Codecov Report
@@ Coverage Diff @@
## master #7858 +/- ##
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- Coverage 86.948% 86.936% -0.013%
- Complexity 36927 36945 +18
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Files 2219 2221 +2
Lines 173673 173803 +130
Branches 18755 18775 +20
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+ Hits 151006 151097 +91
- Misses 16055 16077 +22
- Partials 6612 6629 +17
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Nice work here. I think the index dump tool could be quite useful / educational for some users, but it will need at least an integration test.
Also, a regression test for the bug fix would be ideal.
@droazen any comments on engine class changes or the tool?
| @@ -47,11 +50,15 @@ public FeatureOutputStream( final GATKPath file, | |||
| Utils.nonNull(dict); | |||
| this.encoder = encoder; | |||
| if (IOUtil.hasBlockCompressedExtension(file.toPath())) { | |||
| outputStream = new PositionalOutputStream( | |||
| new BlockCompressedOutputStream(file.toString(), compressionLevel)); | |||
| final BlockCompressedOutputStream bcos = | |||
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For posterity, can you add a comment explaining the necessity for BlockCompressedOutputStream instead of PositionalOutputStream?
| final char meta = (char)readInt(is); | ||
| final int skip = readInt(is); | ||
| final int namesLen = readInt(is); | ||
| System.out.println("#tigs\tformat\tseqCol\tbegCol\tendCol\tmetaChr\tskip"); |
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Preferable to have an output file argument instead of using stdout
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| @Override | ||
| protected Object doWork() { | ||
| try ( final InputStream is = new GZIPInputStream(new FileInputStream(tabixIndexFile)) ) { |
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Add a check that file has extension FileExtensions.TABIX_INDEX
| import java.util.List; | ||
| import java.util.zip.GZIPInputStream; | ||
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| @CommandLineProgramProperties( |
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Add a docstring with explanation and usage, and annotate as a Barclay @DocumentedFeature
| @Argument( doc = "Tabix index file.", | ||
| fullName = "tabix-index", | ||
| shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME) | ||
| String tabixIndexFile; |
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| String tabixIndexFile; | |
| GATKPath tabixIndexFile; |
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@tedsharpe Any chance this might resolve the issue reported in #7838, or is that likely unrelated? |
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@droazen I believe it's unrelated. |
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I believe the review comments are all addressed, and that this is ready to go. (Assuming checks all pass.) |
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