ALS-6330: Fix variant explorer functionality #115
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…erging of variant metadata indexes
…tion test. Fix bug caused by bitmask paddings
Luke-Sikina
reviewed
Oct 9, 2024
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I can't build this
/home/luke/code/bch/pic-sure-hpds/common/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/crypto/CryptoDefaultKeyTest.java:[19,10] cannot find symbol
[ERROR] symbol: class BeforeTestClass
[ERROR] location: class edu.harvard.hms.dbmi.avillach.hpds.crypto.CryptoDefaultKeyTest
What am I doing wrong?
ramari16
commented
Oct 9, 2024
| private static Logger log = LoggerFactory.getLogger(VariantStore.class); | ||
| public static final int BUCKET_SIZE = 1000; | ||
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| public static final String VARIANT_SPEC_INDEX_FILE = "variantSpecIndex.javabin"; | ||
| public static final String VARIANT_SPEC_INDEX_FILE = VARIANT_SPEC_INDEX_JAVABIN_FILENAME; |
ramari16
commented
Oct 9, 2024
| @@ -336,6 +342,7 @@ public PhenoCube<?> load(String key) throws Exception { | |||
| return ret; | |||
| }else { | |||
| log.warn("ColumnMeta not found for : [{}]", key); | |||
| log.info(Joiner.on(",").join(phenotypeMetaStore.getColumnNames())); | |||
ramari16
commented
Oct 9, 2024
| @@ -31,4 +28,7 @@ public interface GenomicProcessor { | |||
| Set<String> getInfoStoreValues(String conceptPath); | |||
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| List<InfoColumnMeta> getInfoColumnMeta(); | |||
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| // todo: make the map value a Set instead of array | |||
ramari16
commented
Oct 9, 2024
| @@ -80,7 +80,7 @@ public VariantIndex load(String infoColumn_valueKey) throws IOException { | |||
| int x = 0; | |||
| for(Integer variantIndex : variantIndexIntArray) { | |||
| // todo: shouldn't this be greater than or equal to 0? 0 is a valid index | |||
ramari16
commented
Oct 9, 2024
| @Test | ||
| public void pathIsVariantSpec_newFormat() { | ||
| assertTrue(VariantUtils.pathIsVariantSpec("chr21,5032061,A,G,LOC102723996,missense_variant")); | ||
| } |
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Add not matching tests
ramari16
commented
Oct 9, 2024
| @@ -1,6 +1,7 @@ | |||
| SMALL_JOB_LIMIT = 100 | |||
| SMALL_TASK_THREADS = 1 | |||
| LARGE_TASK_THREADS = 1 | |||
| VCF_EXCERPT_ENABLED=true | |||
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Rollback until we build new data set
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Variant explorer functionality was broken as part of the initial genomic rewrite. This addresses those issues. Additionally, this adds integration tests from the 1k genome data set (ALS-4643)