Upate to htsjdk 4.0.2 #1413
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Upate to htsjdk 4.0.2 #1413
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This doesn't set the new environment variable yet. |
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The entire "Feature" class/interface structure could use a look, with a view to remove duplicate interfaces wrt the htsjdk. Not for this PR. |
Htsjdk added a new NamedFeature interface that is clashing with IGV's slightly different NamedFeature. Renamed NamedFeature -> IGVNamedFeature Slight change to IGVFeatureReader interface to make it return a CloseableIterator so that it can be handled with try-with-resources.
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Rebased this on master, hopefully the test pass now, it looks like it was some sort of transient issue contacting blast. |
lbergelson
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Oct 31, 2023
| featureList = new ArrayList(); | ||
| featureMap.put(igvChr, featureList); | ||
| } | ||
| List<Feature> featureList = featureMap.computeIfAbsent(igvChr, k -> new ArrayList<>()); |
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I did a bit of refactoring in this method, every where else is basically just renames.
lbergelson
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Oct 31, 2023
| } | ||
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| @Override | ||
| public Iterator<Feature> iterator() throws IOException { | ||
| public CloseableIterator<Feature> iterator() throws IOException { |
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This is autocloseable now so it can be handle automatically.
jrobinso
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Htsjdk added a new NamedFeature interface that is clashing with IGV's slightly different NamedFeature. Renamed NamedFeature -> IGVNamedFeature Slight change to IGVFeatureReader interface to make it return a CloseableIterator so that it can be handled with try-with-resources.
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Htsjdk added a new NamedFeature interface that is clashing with IGV's slightly different NamedFeature. Renamed NamedFeature -> IGVNamedFeature
Slight change to IGVFeatureReader interface to make it return a CloseableIterator so that it can be handled with try-with-resources.
It might be worth updating the new Htsjdk interface to include the displayName() method as well so that can just be used directly?