fix functests

Now that bcftools.sort dispatch does the compression, instead of pysam.tabix_compress, all functest answer files processed by `compress_index_vcf` are not md5sum identical.
ACEnglish · Nov 28, 2024 · b3114a4 · b3114a4
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diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz b/repo_utils/answer_key/bench/bench12/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz b/repo_utils/answer_key/bench/bench12/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz b/repo_utils/answer_key/bench/bench13/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz b/repo_utils/answer_key/bench/bench13/fp.vcf.gz
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diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fp.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench23/fn.vcf.gz b/repo_utils/answer_key/bench/bench23/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench23/fp.vcf.gz b/repo_utils/answer_key/bench/bench23/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_gtcomp_edgecase1/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz b/repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz
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diff --git a/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000000.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000000.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000001.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000001.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000002.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000002.vcf.gz
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diff --git a/repo_utils/answer_key/divide/divided/multi_00000008.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000008.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000009.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000009.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000010.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000010.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000011.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000011.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000012.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000012.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000013.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000013.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000014.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000014.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000015.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000015.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000016.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000016.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000017.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000017.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000018.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000018.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000019.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000019.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000020.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000020.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000021.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000021.vcf.gz
diff --git a/repo_utils/answer_key/divide/divided/multi_00000022.vcf.gz b/repo_utils/answer_key/divide/divided/multi_00000022.vcf.gz
diff --git a/repo_utils/answer_key/ga4gh/ga4gh_norefine_query.vcf.gz b/repo_utils/answer_key/ga4gh/ga4gh_norefine_query.vcf.gz
diff --git a/repo_utils/answer_key/ga4gh/ga4gh_norefine_truth.vcf.gz b/repo_utils/answer_key/ga4gh/ga4gh_norefine_truth.vcf.gz
diff --git a/repo_utils/answer_key/ga4gh/ga4gh_withrefine_query.vcf.gz b/repo_utils/answer_key/ga4gh/ga4gh_withrefine_query.vcf.gz
diff --git a/repo_utils/answer_key/ga4gh/ga4gh_withrefine_truth.vcf.gz b/repo_utils/answer_key/ga4gh/ga4gh_withrefine_truth.vcf.gz
diff --git a/repo_utils/answer_key/phab/phab_result.vcf.gz b/repo_utils/answer_key/phab/phab_result.vcf.gz
diff --git a/repo_utils/answer_key/phab/phab_result_poa.vcf.gz b/repo_utils/answer_key/phab/phab_result_poa.vcf.gz
diff --git a/repo_utils/answer_key/phab/phab_result_wfa.vcf.gz b/repo_utils/answer_key/phab/phab_result_wfa.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/fn.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/fp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/fn.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/fp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_three/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/tp-base.vcf.gz
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diff --git a/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz
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diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz