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TribbleIndexedFeatureReader cannot read header from .bgz files #653

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tomwhite opened this issue Jun 29, 2016 · 3 comments
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TribbleIndexedFeatureReader cannot read header from .bgz files #653

tomwhite opened this issue Jun 29, 2016 · 3 comments
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@tomwhite
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TribbleIndexedFeatureReader.isGZIPPath only recognizes paths ending in .gz, so block gzip-compressed files are not picked up.

The fix is to check for any of the extensions defined in AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS rather than just .gz.
@tomwhite tomwhite mentioned this issue Jun 29, 2016
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@magicDGS
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This could be close, couldn't it?

@cmnbroad cmnbroad self-assigned this Jul 27, 2016
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cmnbroad commented Jul 27, 2016 •
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@magicDGS The change @tomwhite made was for Hadoop-BAM. This still needs to be fixed in htsjdk.

@magicDGS
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I can take this ticket, because it is easy to fix. So thanks for the answer, @cmnbroad!

@magicDGS magicDGS mentioned this issue Jul 27, 2016
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jamesemery pushed a commit to jamesemery/htsjdk that referenced this issue Sep 1, 2016
@magicDGS @jamesemery
Fix samtools#653 (samtools#672)
ffd8427 
* added checking for AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS in TribbleIndexedFeatureReader

* fixing WFIterator checking of compressed file

* isGZIPPath deprecation

* added test for new functionality

* fixing URL encoding

* added no-remote test file with spaces
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@tomwhite @magicDGS @cmnbroad