PrintBGZFBlockInformation: remove file extension check so that we can accept, eg., bams #5801
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… accept, eg., bams The file extension check in this tool was redundant, since there is a subsequent check that the input file is in BGZF format. Resolves #5800
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@jamesemery please review (@kvg ran into this issue yesterday) |
Codecov Report
@@ Coverage Diff @@
## master #5801 +/- ##
===============================================
- Coverage 87.002% 85.583% -1.419%
+ Complexity 32111 31394 -717
===============================================
Files 1974 1977 +3
Lines 147246 147095 -151
Branches 16217 16170 -47
===============================================
- Hits 128107 125888 -2219
- Misses 13233 15211 +1978
- Partials 5906 5996 +90
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jamesemery
reviewed
Mar 15, 2019
| @@ -71,11 +71,6 @@ protected void onStartup() { | |||
| throw new UserException.CouldNotReadInputFile("File " + bgzfPathString + " does not exist"); | |||
| } | |||
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| if ( ! IOUtil.hasBlockCompressedExtension(bgzfPathString) ) { | |||
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Maybe you should amend the below statement "File is not a valid BGZF file. Could possibly be a regular GZIP file?" to better reflect that the user may have provided any file under the sun.
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I would also explicitly add a reference to the javadocs for this tool that mentions the bam use case as it sounds incredibly useful to people.
| @@ -100,4 +100,20 @@ public void testRegularGzipFile() throws IOException { | |||
| }; | |||
| runCommandLine(args); | |||
| } | |||
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| /* Make sure that we can handle a standard BAM file */ | |||
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Maybe add a test to ensure there is a nice exception when the user provides a non-BGZF file (maybe a VCF).
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@jamesemery Comments addressed, back to you. |
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The file extension check in this tool was redundant, since there is a subsequent check
that the input file is in BGZF format.
Resolves #5800