Cleaning up old interval code #6465
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* Currently things are in a weird state, picard style interval lists are handled either as tribble files if they are named correctly as .interval_list If they are named .intervals, .picard, or .list they are loaded with a different code path. This unifies it so that picard files are only loaded as .interval_list and .intervals is always considered a Gatk style list * This removes the work around for broken 0 length intervals that was put in place a long time ago. However, the workaround was effectively removed for all .interval_list files in 4.1.3.0 when we started reading those through the tribble plugin. Either the broken files no longer are used or they are misnamed as .intervals * fix tests to deal correctly with .inverval_list vs .intervals
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relevant issue is #2520 |
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@cmnbroad Maybe you can review this one? |
cmnbroad
approved these changes
Feb 28, 2020
| // If it's neither a Feature-containing file nor an interval file, but is an existing file, throw an error. | ||
| // Note that since contigs can contain periods in their names, we can't use the mere presence of an "extension" | ||
| // as evidence that the user intended the String to be interpreted as a file. | ||
| else if ( new File(arg).exists() ) { | ||
| throw new UserException.CouldNotReadInputFile(arg, String.format("The file %s exists, but does not contain Features " + | ||
| "(ie., is not in a supported Feature file format such as vcf, bcf, or bed), " + | ||
| "and does not have one of the supported interval file extensions (" + INTERVAL_FILE_EXTENSIONS + "). " + | ||
| "and does not have one of the supported interval file extensions (" + GATK_INTERVAL_FILE_EXTENSIONS + "). " + |
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Kind of a nit, but this error message will no longer include ".interval_list", which is an acceptable extension.
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technically interval_list is a feature file now
| } | ||
| return ret; | ||
| } catch (final UserException e){ | ||
| throw e; |
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This block seems unnecessary ? It might be better to just rely on the next catch block, which will always include the inputPath name.
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I think I thought it might replace a more specific error with a less specific one. Since userexceptions don't show the stack trace you'd lose the underlying one in most cases.
lbergelson
commented
Feb 28, 2020
src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
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Currently things are in a weird state, picard style interval lists are handled either as tribble files if they are named correctly as .interval_list
If they are named .intervals, .picard, or .list they are loaded with a different code path.
This unifies it so that picard files are only loaded as .interval_list and .intervals is always considered a Gatk style list
This removes the work around for broken 0 length intervals that was put in place a long time ago. However, the workaround was effectively removed
for all .interval_list files in 4.1.3.0 when we started reading those through the tribble plugin. Either the broken files no longer are used or they
are misnamed as .intervals
fix tests to deal correctly with .inverval_list vs .intervals