Path-enable IndexFactory. #1430
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Codecov Report
@@ Coverage Diff @@
## master #1430 +/- ##
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- Coverage 68.359% 68.35% -0.009%
- Complexity 8486 8489 +3
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Files 583 583
Lines 34373 34389 +16
Branches 5730 5729 -1
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+ Hits 23497 23505 +8
- Misses 8655 8665 +10
+ Partials 2221 2219 -2
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@cmnbroad Thank you for doing this. I see this includes Jonn's change. Should we wait for that to go in before merging this?
| @@ -224,7 +229,20 @@ else if (indexFile.endsWith(FileExtensions.TABIX_INDEX)) { | |||
| * @param codec the codec to use for decoding records | |||
| */ | |||
| public static LinearIndex createLinearIndex(final File inputFile, final FeatureCodec codec) { | |||
| return createLinearIndex(inputFile, codec, LinearIndexCreator.DEFAULT_BIN_WIDTH); | |||
| return createLinearIndex( | |||
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You can use IOUtil.toPath(file) which does a null safe conversion to path and then just have the null check in the final one.
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| // We _MUST_ call getPathToDataFile here to preserve behavior of codecs that rely on config files | ||
| // that point to other files to be indexed. This is CRITICALLY IMPORTANT to downstream tools. | ||
| this.inputPath = Paths.get(codec.getPathToDataFile(inputPath.toUri().toString())); |
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ugh... path -> uri -> string -> string -> path Not much to do about it though :(
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Yeah, I considered changing getPathToDataFile to return a Path instead of a String, but decided that was too much scope creep.
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@lbergelson I don't think the order in which we merge these matters, but we should probably wait for @jonn-smith 's redirect test before we merge either one. |
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Sorry, I merged mine which caused a conflict :( |
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@cmnbroad I merged the xsv fix. |
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@lbergelson Rebased and conflicts resolved. |
* While adding Path variants of File methods in #1430 we accidentally replaced a method instead of adding a new one. * Add that method back in and 1 additional overload which we missed.
Prerequisite for broadinstitute/gatk#6161.