Load BlockCompressedIndexedFastaSequenceFile and GZIIndex from streams #1259
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…ted from streams. This enables fasta.gz files to be loaded from streams.
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cc @lbergelson |
Codecov Report
@@ Coverage Diff @@
## master #1259 +/- ##
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- Coverage 69.356% 67.496% -1.86%
+ Complexity 8164 8153 -11
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Files 548 558 +10
Lines 32675 33374 +699
Branches 5520 5609 +89
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- Hits 22662 22526 -136
- Misses 7795 8658 +863
+ Partials 2218 2190 -28
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@tomwhite This looks good. It needs some additional javadoc and then is good to merge.
| @@ -75,6 +78,15 @@ public BlockCompressedIndexedFastaSequenceFile(final Path path, final FastaSeque | |||
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| public BlockCompressedIndexedFastaSequenceFile(final String source, final SeekableStream in, final FastaSequenceIndex index, final SAMSequenceDictionary dictionary, final GZIIndex gziIndex) { | |||
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javadoc, mention that the stream shouldn't be decompressed already
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Huh, it looks like there might be a bug in the previous constructor where it calls canCreateBZlockCompressedIndexedFastaSequence(). That checks that there's a gzi file in the appropriate location relative to Path even though it has the GZI index passed in... I opened a #1290 to track that...
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| * @throws IOException if an I/O error occurs. | ||
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| public static final GZIIndex loadIndex(final String source, final InputStream indexIn) throws IOException { |
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mention that source is used for error messages in the doc and can be null
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this is silly, but can you put the InputStream as the first parameter since it's the important one
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Fixed the javadoc.
However, I left source as the first parameter for consistency with BlockCompressedIndexedFastaSequenceFile, ReferenceSequenceFileFactory, VariantContext, tribble's IndexFactory, etc.
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| public static final GZIIndex loadIndex(final String source, final ReadableByteChannel channel) throws IOException { |
Description
This enables fasta.gz files to be loaded from streams (not just path objects), which is needed for disq-bio/disq#75.
See original bug report in broadinstitute/gatk#5547
Checklist