From 58d2262b7a9765290006e06c2cfabe9c5b054f48 Mon Sep 17 00:00:00 2001 From: James Date: Wed, 7 Jun 2023 11:45:44 -0400 Subject: [PATCH] cleanup --- .../utils/codecs/gtf/GencodeGtfCodecUnitTest.java | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java index ef0cd36803c..b99f17cd94e 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java @@ -3362,14 +3362,6 @@ private Object[] createTestData_gencode_v19_and_this_is_a_valid_one_too() { }; } -// private Object[] createTestData_gencode_v43_valid_gencode() { -// return new Object[] { -// "gencode.v19.and.this.is.a.valid.one.too.gtf", -// new ArrayList<>( Collections.singletonList( createGencodeGtfGene_gencode_v19_and_this_is_a_valid_one_too() ) ), -// "hg19" -// }; -// } - // ============================================================================================================ // ============================================================================================================ // ============================================================================================================ @@ -3400,7 +3392,7 @@ private Object[][] testIndexingProvider() { { gencodeHG38V43TestFile, "chr1", 35001, 35500, 1, }, // region fits in gene { gencodeHG38V43TestFile, "chr1", 35500, 37000, 1, }, // region start in gene { gencodeHG38V43TestFile, "chr1", 32198, 35500, 1, }, // region end in gene - { gencodeHG38V43TestFile, "chr1", 1, 200000000, 1982, }, // Many genes in region + { gencodeHG38V43TestFile, "chr1", 1, 200000000, 677, }, // Many genes in region { gencodeHG38V43TestFile, "chr1", 33001, 34091, 0, }, // no genes in region @@ -3455,7 +3447,7 @@ public Object[][] canDecodeProvider() { { "gencode.valid_gencode_file2.gtf" , testResourceDir, true}, // Valid file { "gencode.and.this.is.a.valid.one.too.table.gtf", testResourceDir, true}, // Valid file - //{ "gencode.v43.LargeFile.gtf" , largeFileTestDir, true}, // Valid file - v43 (with previously disallowed tags) + { "gencode.v43.LargeFile.gtf" , largeFileTestDir, true}, // Valid file - v43 (with previously disallowed tags) { "Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.44.gtf", eColiTestDir, false}, // Not valid GENCODE GTF };