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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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@tomwhite @magicDGS @cmnbroad
@tomwhite
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tomwhite commented Jun 29, 2016

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 referenced this issue in HadoopGenomics/Hadoop-BAM Jun 29, 2016

Merged

Add BGZFCodec for reading and writing files with a .bgz suffix. #106

@magicDGS
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magicDGS commented Jul 27, 2016

This could be close, couldn't it?

cmnbroad self-assigned this Jul 27, 2016

@cmnbroad
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cmnbroad commented Jul 27, 2016 • edited

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

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

magicDGS referenced this issue Jul 27, 2016

Merged

Fix #653 #672

yfarjoun closed this in c8202f2 Aug 10, 2016

@jamesemery jamesemery added a commit to jamesemery/htsjdk that referenced this issue Sep 1, 2016

@magicDGS @jamesemery magicDGS + jamesemery Fix #653 (#672) 
* 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
 ffd8427
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