diff --git a/repo_utils/answer_key/phab/phab_result.vcf.gz b/repo_utils/answer_key/phab/phab_result.vcf.gz
index 38ccaf41..64267d56 100644
Binary files a/repo_utils/answer_key/phab/phab_result.vcf.gz and b/repo_utils/answer_key/phab/phab_result.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/log.txt b/repo_utils/answer_key/refine/refine_output_one/log.txt
index bfb7ced7..672b1248 100644
--- a/repo_utils/answer_key/refine/refine_output_one/log.txt
+++ b/repo_utils/answer_key/refine/refine_output_one/log.txt
@@ -1,6 +1,6 @@
-2023-11-01 14:04:28,717 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
-2023-11-01 14:04:28,719 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_one
-2023-11-01 14:04:28,720 [INFO] Params:
+2023-12-19 15:33:50,086 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:33:50,088 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_one
+2023-12-19 15:33:50,089 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz",
     "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz",
@@ -28,10 +28,10 @@
     "check_monref": true,
     "check_multi": true
 }
-2023-11-01 14:04:28,793 [INFO] Including 225 bed regions
-2023-11-01 14:04:30,301 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
-2023-11-01 14:04:30,302 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
-2023-11-01 14:04:30,471 [INFO] Stats: {
+2023-12-19 15:33:50,173 [INFO] Including 225 bed regions
+2023-12-19 15:33:51,903 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
+2023-12-19 15:33:51,904 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
+2023-12-19 15:33:52,077 [INFO] Stats: {
     "TP-base": 387,
     "TP-comp": 387,
     "FP": 64,
@@ -83,4 +83,4 @@
         }
     }
 }
-2023-11-01 14:04:30,472 [INFO] Finished bench
+2023-12-19 15:33:52,078 [INFO] Finished bench
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
index 96164456..12e40b35 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi
index 1fe966ae..4c6a2607 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed b/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed
index 355b2b4a..da120214 100644
--- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed
+++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed
@@ -1,9 +1,5 @@
 chr20	5040476	5040477
 chr20	5041941	5042433
-chr20	7720952	7720968
 chr20	16257854	16259205
-chr20	24682040	24682100
-chr20	51953819	51953820
-chr20	55627638	55628305
-chr20	63028079	63029030
-chr20	64134990	64135242
\ No newline at end of file
+chr20	32723044	32723045
+chr20	51953819	51953820
\ No newline at end of file
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
index 886198e7..73f87a20 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi
index 594d962f..31e4f39e 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fn.vcf.gz.tbi differ
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
index 4da7646d..63d62d0c 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi
index 0c9b564a..f5300778 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json
index 781e66c6..5463076f 100644
--- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json
+++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json
@@ -1 +1 @@
-{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/c7gxuj5a.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
+{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/yw_a31jd.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json
index 0d92566a..e25434c6 100644
--- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json
+++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json
@@ -1,48 +1,47 @@
 {
-    "TP-base": 379,
-    "TP-comp": 379,
-    "FP": 7,
-    "FN": 3,
-    "precision": 0.9818652849740933,
-    "recall": 0.9921465968586387,
-    "f1": 0.9869791666666666,
-    "base cnt": 382,
-    "comp cnt": 386,
-    "TP-comp_TP-gt": 379,
+    "TP-base": 381,
+    "TP-comp": 381,
+    "FP": 4,
+    "FN": 2,
+    "precision": 0.9896103896103896,
+    "recall": 0.9947780678851175,
+    "f1": 0.9921875,
+    "base cnt": 383,
+    "comp cnt": 385,
+    "TP-comp_TP-gt": 381,
     "TP-comp_FP-gt": 0,
-    "TP-base_TP-gt": 379,
+    "TP-base_TP-gt": 381,
     "TP-base_FP-gt": 0,
     "gt_concordance": 1.0,
     "gt_matrix": {
         "(0, 1)": {
-            "(1, 0)": 143
+            "(1, 0)": 145
         },
         "(1, 0)": {
-            "(0, 1)": 184,
-            "(1, 0)": 1
+            "(0, 1)": 184
         },
         "(1, 1)": {
-            "(1, 1)": 51
+            "(1, 1)": 52
         }
     },
     "weighted": {
         "sequence": {
-            "TP": 384.0702000260353,
-            "FP": 4.3610000014305115,
-            "FN": 0.5952999591827393,
-            "precision": 0.9887727865291919,
-            "recall": 0.9984524217555106,
-            "f1": 0.9935890297287107,
-            "total": 389
+            "TP": 382.03810000419617,
+            "FP": 3.716600000858307,
+            "FN": 1.2736999988555908,
+            "precision": 0.9903653798623592,
+            "recall": 0.9966771176915361,
+            "f1": 0.9935112243223944,
+            "total": 387
         },
         "size": {
-            "TP": 384.2482999712229,
-            "FP": 4.497000023722649,
-            "FN": 0.2547000050544739,
-            "precision": 0.9884320144223451,
-            "recall": 0.9993375864295723,
-            "f1": 0.9938548846095698,
-            "total": 389
+            "TP": 382.14099998772144,
+            "FP": 3.820500001311302,
+            "FN": 1.0385000109672546,
+            "precision": 0.990101344301388,
+            "recall": 0.9972897819142965,
+            "f1": 0.9936825627390087,
+            "total": 387
         }
     }
 }
\ No newline at end of file
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
index 2a2d3326..ec079583 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi
index 03d9aa8f..db84618f 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz.tbi differ
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
index f37cfd32..913f7adb 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi
index 09951382..7ebf847d 100644
Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-comp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.log.txt b/repo_utils/answer_key/refine/refine_output_one/refine.log.txt
index e72704e7..597f25d5 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.log.txt
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.log.txt
@@ -1,6 +1,6 @@
-2023-11-01 14:04:32,128 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
-2023-11-01 14:04:32,129 [INFO] Command /data/truvari/__main__.py refine -u -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one
-2023-11-01 14:04:32,131 [INFO] Params:
+2023-12-19 15:33:53,701 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:33:53,702 [INFO] Command /data/truvari/__main__.py refine -u -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one
+2023-12-19 15:33:53,703 [INFO] Params:
 {
     "benchdir": "test_results/refine_output_one",
     "reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
@@ -13,17 +13,17 @@
     "mafft_params": "--auto --thread 1",
     "debug": false
 }
-2023-11-01 14:04:32,132 [INFO] Setting up regions
-2023-11-01 14:04:32,154 [INFO] Evaluating 225 regions
-2023-11-01 14:04:32,712 [INFO] 85 regions to be refined
-2023-11-01 14:04:32,757 [INFO] Preparing regions
-2023-11-01 14:04:32,769 [INFO] Extracting haplotypes
-2023-11-01 14:05:28,548 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
-2023-11-01 14:05:28,553 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
-2023-11-01 14:05:28,557 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
-2023-11-01 14:05:28,651 [INFO] Harmonizing variants
-2023-11-01 14:05:31,650 [INFO] Running bench
-2023-11-01 14:05:31,716 [INFO] Including 85 bed regions
-2023-11-01 14:05:32,942 [INFO] Zipped 4154 variants Counter({'base': 2077, 'comp': 2077})
-2023-11-01 14:05:32,943 [INFO] 85 chunks of 4154 variants Counter({'__filtered': 3386, 'comp': 386, 'base': 382})
-2023-11-01 14:05:33,483 [INFO] Finished refine
+2023-12-19 15:33:53,704 [INFO] Setting up regions
+2023-12-19 15:33:53,725 [INFO] Evaluating 225 regions
+2023-12-19 15:33:54,307 [INFO] 85 regions to be refined
+2023-12-19 15:33:54,344 [INFO] Preparing regions
+2023-12-19 15:33:54,354 [INFO] Extracting haplotypes
+2023-12-19 15:33:55,039 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:33:55,041 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:33:55,154 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:33:55,162 [INFO] Harmonizing variants
+2023-12-19 15:33:57,833 [INFO] Running bench
+2023-12-19 15:33:57,887 [INFO] Including 85 bed regions
+2023-12-19 15:33:59,098 [INFO] Zipped 4106 variants Counter({'base': 2053, 'comp': 2053})
+2023-12-19 15:33:59,100 [INFO] 86 chunks of 4106 variants Counter({'__filtered': 3338, 'comp': 385, 'base': 383})
+2023-12-19 15:33:59,647 [INFO] Finished refine
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
index d9692fde..1abab8da 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 194,
-    "TN": 15,
-    "FP": 13,
-    "FN": 3,
-    "base P": 201,
-    "base N": 24,
+    "TP": 199,
+    "TN": 14,
+    "FP": 10,
+    "FN": 2,
+    "base P": 202,
+    "base N": 23,
     "comp P": 210,
     "comp N": 15,
-    "PPV": 0.9238095238095239,
-    "TPR": 0.9651741293532339,
-    "TNR": 0.625,
-    "NPV": 1.0,
-    "ACC": 0.9288888888888889,
-    "BA": 0.7950870646766169,
-    "F1": 0.9440389294403894,
+    "PPV": 0.9476190476190476,
+    "TPR": 0.9851485148514851,
+    "TNR": 0.6086956521739131,
+    "NPV": 0.9333333333333333,
+    "ACC": 0.9466666666666667,
+    "BA": 0.7969220835126991,
+    "F1": 0.9660194174757282,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
index c0de0125..4c665b54 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
@@ -19,7 +19,7 @@ chr20	5554104	5554185	0	0	0	0	False	0	0	0	0	TN
 chr20	5962327	5962410	0	0	0	0	False	0	0	0	0	TN
 chr20	7435215	7435749	2	2	0	0	False	2	2	0	0	TP
 chr20	7719330	7719414	1	1	0	0	False	1	1	0	0	TP
-chr20	7720911	7721003	1	1	1	0	True	1	1	1	0	FN
+chr20	7720911	7721003	1	1	1	0	True	1	1	0	0	TP
 chr20	7721059	7721319	0	0	0	0	False	0	0	0	0	TN
 chr20	8661911	8662657	1	1	3	1	True	9	9	0	0	TP
 chr20	9015548	9016039	1	1	0	0	False	1	1	0	0	TP
@@ -55,7 +55,7 @@ chr20	23267965	23268087	2	2	0	0	False	2	2	0	0	TP
 chr20	23560883	23561191	1	1	2	2	True	3	3	0	0	TP
 chr20	23942431	23942955	1	1	0	0	False	1	1	0	0	TP
 chr20	24407983	24408997	3	3	1	0	True	2	2	0	0	TP
-chr20	24681988	24682277	2	2	1	0	True	1	1	0	1	FP
+chr20	24681988	24682277	2	2	1	0	True	2	2	0	0	TP
 chr20	24836081	24836384	2	2	0	0	False	2	2	0	0	TP
 chr20	24956961	24957198	2	2	0	0	False	2	2	0	0	TP
 chr20	24982027	24982423	1	1	0	0	False	1	1	0	0	TP
@@ -66,7 +66,7 @@ chr20	29401872	29402283	0	0	0	0	False	0	0	0	0	TN
 chr20	29799755	29799978	0	0	0	0	False	0	0	0	0	TN
 chr20	30404513	30406201	0	0	0	0	False	0	0	0	0	TN
 chr20	31689079	31689527	2	2	0	0	False	2	2	0	0	TP
-chr20	32722424	32723212	0	0	1	0	True	0	0	0	0	TN
+chr20	32722424	32723212	0	0	1	0	True	0	0	1	0	FN
 chr20	32723469	32724637	0	0	0	0	False	0	0	0	0	TN
 chr20	32724927	32724999	0	0	0	0	False	0	0	0	0	TN
 chr20	34205619	34205960	1	1	0	0	False	1	1	0	0	TP
@@ -113,7 +113,7 @@ chr20	53913028	53913352	2	2	0	0	False	2	2	0	0	TP
 chr20	54690771	54690873	2	2	0	0	False	2	2	0	0	TP
 chr20	55532159	55533378	1	1	0	0	False	1	1	0	0	TP
 chr20	55624482	55625807	6	6	6	0	True	11	11	0	0	TP
-chr20	55627344	55628450	7	7	4	0	True	7	7	0	1	FP
+chr20	55627344	55628450	7	7	4	0	True	8	8	0	0	TP
 chr20	55943919	55945807	2	2	2	1	True	5	5	0	0	TP
 chr20	56280422	56282114	4	4	5	1	True	10	10	0	0	TP
 chr20	56284258	56284407	2	2	0	0	False	2	2	0	0	TP
@@ -172,7 +172,7 @@ chr20	62875172	62875556	2	2	3	0	True	3	3	0	0	TP
 chr20	62975788	62976224	1	1	0	0	False	1	1	0	0	TP
 chr20	62986310	62986805	2	2	0	0	False	2	2	0	0	TP
 chr20	63027997	63028166	2	2	1	0	True	4	4	0	0	TP
-chr20	63028876	63029402	2	2	0	1	True	1	1	0	1	FP
+chr20	63028876	63029402	2	2	0	1	True	2	2	0	0	TP
 chr20	63049033	63049412	3	3	1	0	True	2	2	0	0	TP
 chr20	63068409	63068799	2	2	0	0	False	2	2	0	0	TP
 chr20	63103249	63103492	1	1	0	0	False	1	1	0	0	TP
@@ -219,8 +219,8 @@ chr20	64090704	64091389	0	0	0	2	False	0	0	0	2	FP
 chr20	64096658	64097164	0	0	0	2	False	0	0	0	2	FP
 chr20	64125109	64127974	3	3	3	0	True	12	12	0	0	TP
 chr20	64131804	64133955	5	5	8	1	True	24	24	0	0	TP
-chr20	64134883	64136386	3	3	1	0	True	4	4	1	0	FN
+chr20	64134883	64136386	3	3	1	0	True	4	4	0	0	TP
 chr20	64157894	64158976	2	2	0	0	False	2	2	0	0	TP
-chr20	64173409	64176529	4	4	7	3	True	18	18	0	0	TP
+chr20	64173409	64176529	4	4	7	3	True	17	17	0	0	TP
 chr20	64201854	64202098	3	3	0	0	False	3	3	0	0	TP
 chr20	64233048	64233545	2	2	0	0	False	2	2	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
index e61085c2..edc91450 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 591,
-    "TP-comp": 591,
-    "FP": 18,
-    "FN": 3,
-    "precision": 0.9704433497536946,
-    "recall": 0.9949494949494949,
-    "f1": 0.9825436408977556,
-    "base cnt": 594,
-    "comp cnt": 609
+    "TP-base": 593,
+    "TP-comp": 593,
+    "FP": 15,
+    "FN": 2,
+    "precision": 0.975328947368421,
+    "recall": 0.9966386554621849,
+    "f1": 0.9858686616791356,
+    "base cnt": 595,
+    "comp cnt": 608
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_three/log.txt b/repo_utils/answer_key/refine/refine_output_three/log.txt
index c4110bc2..e6bd2d31 100644
--- a/repo_utils/answer_key/refine/refine_output_three/log.txt
+++ b/repo_utils/answer_key/refine/refine_output_three/log.txt
@@ -1,6 +1,6 @@
-2023-11-01 14:06:18,612 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
-2023-11-01 14:06:18,613 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_three
-2023-11-01 14:06:18,614 [INFO] Params:
+2023-12-19 15:34:12,422 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:34:12,423 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_three
+2023-12-19 15:34:12,425 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz",
     "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz",
@@ -28,10 +28,10 @@
     "check_monref": true,
     "check_multi": true
 }
-2023-11-01 14:06:18,683 [INFO] Including 225 bed regions
-2023-11-01 14:06:20,271 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
-2023-11-01 14:06:20,272 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
-2023-11-01 14:06:20,478 [INFO] Stats: {
+2023-12-19 15:34:12,508 [INFO] Including 225 bed regions
+2023-12-19 15:34:14,248 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
+2023-12-19 15:34:14,250 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
+2023-12-19 15:34:14,462 [INFO] Stats: {
     "TP-base": 387,
     "TP-comp": 387,
     "FP": 64,
@@ -83,4 +83,4 @@
         }
     }
 }
-2023-11-01 14:06:20,479 [INFO] Finished bench
+2023-12-19 15:34:14,463 [INFO] Finished bench
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
index a934c83d..d42e536f 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi
index 0f71574c..d423dd20 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi differ
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
index d19ac02d..10f87aaf 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi
index 7d794f6f..4d0fb4ae 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi differ
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
index ae9977d6..0f35b523 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi
index 08a57ccc..834228c5 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json
index 43197620..db270a03 100644
--- a/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json
+++ b/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json
@@ -1 +1 @@
-{"base": "test_results/refine_output_three/phab.output.vcf.gz", "comp": "test_results/refine_output_three/phab.output.vcf.gz", "output": "test_results/refine_output_three/phab_bench", "includebed": "/tmp/ce30u761.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
+{"base": "test_results/refine_output_three/phab.output.vcf.gz", "comp": "test_results/refine_output_three/phab.output.vcf.gz", "output": "test_results/refine_output_three/phab_bench", "includebed": "/tmp/fqzb0b6u.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json
index a9fff9f2..c89425b0 100644
--- a/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json
+++ b/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json
@@ -29,21 +29,21 @@
     },
     "weighted": {
         "sequence": {
-            "TP": 120.4527998296544,
-            "FP": 9.857900094240904,
-            "FN": 17.068500188179314,
-            "precision": 0.9243508008168312,
-            "recall": 0.8758846797843979,
-            "f1": 0.8994653354032435,
+            "TP": 121.03439995925874,
+            "FP": 9.64990008994937,
+            "FN": 16.475100067444146,
+            "precision": 0.9261586886388359,
+            "recall": 0.8801893682673207,
+            "f1": 0.9025890973244014,
             "total": 139
         },
         "size": {
-            "TP": 117.62869990803301,
+            "TP": 117.65679998137057,
             "FP": 11.260100107640028,
-            "FN": 19.847500076517463,
-            "precision": 0.9126370940976192,
-            "recall": 0.8556295556703785,
-            "f1": 0.8832143855831983,
+            "FN": 19.819400003179908,
+            "precision": 0.9126561366285918,
+            "recall": 0.855833955219833,
+            "f1": 0.8833321880249987,
             "total": 139
         }
     }
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
index 101e2160..8316f0f7 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi
index b830017a..bcccf78b 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi differ
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
index 3a400e55..1877d571 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi
index 43dc3ea1..899b5452 100644
Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.log.txt b/repo_utils/answer_key/refine/refine_output_three/refine.log.txt
index 861343e0..82c2c64d 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.log.txt
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.log.txt
@@ -1,6 +1,6 @@
-2023-11-01 14:06:22,093 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
-2023-11-01 14:06:22,094 [INFO] Command /data/truvari/__main__.py refine --recount -U -r test_results/refine_output_three/candidate.refine.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_three
-2023-11-01 14:06:22,095 [INFO] Params:
+2023-12-19 15:34:16,211 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:34:16,213 [INFO] Command /data/truvari/__main__.py refine --recount -U -r test_results/refine_output_three/candidate.refine.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_three
+2023-12-19 15:34:16,214 [INFO] Params:
 {
     "benchdir": "test_results/refine_output_three",
     "reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
@@ -13,14 +13,16 @@
     "mafft_params": "--auto --thread 1",
     "debug": false
 }
-2023-11-01 14:06:22,096 [INFO] Setting up regions
-2023-11-01 14:06:22,144 [INFO] 92 --regions reduced to 92 after intersecting with 225 from --includebed
-2023-11-01 14:06:22,523 [INFO] 41 regions to be refined
-2023-11-01 14:06:22,532 [INFO] Preparing regions
-2023-11-01 14:06:22,537 [INFO] Extracting haplotypes
-2023-11-01 14:06:23,106 [INFO] Harmonizing variants
-2023-11-01 14:06:24,655 [INFO] Running bench
-2023-11-01 14:06:24,706 [INFO] Including 41 bed regions
-2023-11-01 14:06:25,093 [INFO] Zipped 2844 variants Counter({'base': 1422, 'comp': 1422})
-2023-11-01 14:06:25,094 [INFO] 35 chunks of 2844 variants Counter({'__filtered': 2595, 'base': 136, 'comp': 113})
-2023-11-01 14:06:26,429 [INFO] Finished refine
+2023-12-19 15:34:16,216 [INFO] Setting up regions
+2023-12-19 15:34:16,264 [INFO] 92 --regions reduced to 92 after intersecting with 225 from --includebed
+2023-12-19 15:34:16,681 [INFO] 41 regions to be refined
+2023-12-19 15:34:16,691 [INFO] Preparing regions
+2023-12-19 15:34:16,696 [INFO] Extracting haplotypes
+2023-12-19 15:34:17,133 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:34:17,155 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:34:17,169 [INFO] Harmonizing variants
+2023-12-19 15:34:18,825 [INFO] Running bench
+2023-12-19 15:34:18,872 [INFO] Including 41 bed regions
+2023-12-19 15:34:19,325 [INFO] Zipped 2824 variants Counter({'base': 1412, 'comp': 1412})
+2023-12-19 15:34:19,327 [INFO] 35 chunks of 2824 variants Counter({'__filtered': 2573, 'base': 136, 'comp': 115})
+2023-12-19 15:34:20,774 [INFO] Finished refine
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
index 1be00983..6003cac7 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 15,
+    "TP": 17,
     "TN": 6,
-    "FP": 25,
+    "FP": 23,
     "FN": 58,
     "base P": 76,
     "base N": 16,
     "comp P": 85,
     "comp N": 7,
-    "PPV": 0.17647058823529413,
-    "TPR": 0.19736842105263158,
+    "PPV": 0.2,
+    "TPR": 0.2236842105263158,
     "TNR": 0.375,
     "NPV": 0.8571428571428571,
-    "ACC": 0.22826086956521738,
-    "BA": 0.2861842105263158,
-    "F1": 0.1863354037267081,
+    "ACC": 0.25,
+    "BA": 0.2993421052631579,
+    "F1": 0.2111801242236025,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
index 4ac24492..1498de92 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
@@ -15,8 +15,8 @@ chr20	16395201	16395373	3	3	1	0	False	3	3	1	0	FN
 chr20	17081293	17081365	2	2	1	0	False	2	2	1	0	FN
 chr20	18209139	18210134	3	3	2	1	True	3	3	0	1	FP
 chr20	20296014	20296330	2	2	2	1	True	5	5	0	0	TP
-chr20	20320339	20320519	1	1	2	1	True	1	1	0	1	FP
-chr20	20337285	20337624	1	1	6	2	True	2	2	0	1	FP
+chr20	20320339	20320519	1	1	2	1	True	3	3	0	0	TP
+chr20	20337285	20337624	1	1	6	2	True	1	1	0	0	TP
 chr20	20354912	20355435	3	3	1	0	False	3	3	1	0	FN
 chr20	20356530	20357810	4	4	8	1	True	8	8	2	0	FN
 chr20	21120298	21120461	2	2	1	0	False	2	2	1	0	FN
@@ -46,7 +46,7 @@ chr20	53204099	53204252	2	2	2	1	True	0	0	0	0	TN
 chr20	55624808	55625652	6	6	6	0	False	6	6	6	0	FN
 chr20	55627638	55628305	7	7	4	0	False	7	7	4	0	FN
 chr20	55944272	55945175	2	2	2	1	True	1	1	2	0	FN
-chr20	56280541	56281913	4	4	5	1	True	3	3	2	1	FN,FP
+chr20	56280541	56281913	4	4	5	1	True	4	4	2	1	FN,FP
 chr20	57090868	57091166	1	1	2	0	False	1	1	2	0	FN
 chr20	57110450	57110593	2	2	1	0	False	2	2	1	0	FN
 chr20	57190256	57190428	0	0	3	1	True	0	0	0	0	TN
@@ -67,7 +67,7 @@ chr20	62057602	62058768	1	1	3	1	True	1	1	0	0	TP
 chr20	62270413	62270827	1	1	3	1	True	3	3	0	0	TP
 chr20	62321396	62321730	2	2	3	0	False	2	2	3	0	FN
 chr20	62349641	62349826	1	1	5	1	True	0	0	2	1	FN,FP
-chr20	62360410	62360602	0	0	8	2	True	0	0	6	1	FN,FP
+chr20	62360410	62360602	0	0	8	2	True	2	2	2	1	FN,FP
 chr20	62830650	62830697	2	2	1	1	True	1	1	0	0	TP
 chr20	62875241	62875404	2	2	3	0	False	2	2	3	0	FN
 chr20	63028066	63029030	4	4	1	1	True	2	2	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
index 1a23dd9a..c4e13143 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 404,
-    "TP-comp": 404,
-    "FP": 37,
-    "FN": 112,
-    "precision": 0.9160997732426304,
-    "recall": 0.7829457364341085,
-    "f1": 0.8443051201671891,
+    "TP-base": 408,
+    "TP-comp": 408,
+    "FP": 35,
+    "FN": 108,
+    "precision": 0.9209932279909706,
+    "recall": 0.7906976744186046,
+    "f1": 0.8508863399374348,
     "base cnt": 516,
-    "comp cnt": 441
+    "comp cnt": 443
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/candidate.refine.bed b/repo_utils/answer_key/refine/refine_output_two/candidate.refine.bed
new file mode 100644
index 00000000..3da282b1
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/candidate.refine.bed
@@ -0,0 +1,92 @@
+chr20	278929	279069
+chr20	641912	642420
+chr20	2240960	2241290
+chr20	4032357	4033228
+chr20	5040476	5040477
+chr20	5041941	5042268
+chr20	7720952	7720968
+chr20	8661944	8662119
+chr20	10802727	10802844
+chr20	13848272	13848544
+chr20	14862054	14862644
+chr20	16257854	16259205
+chr20	16395201	16395373
+chr20	17081293	17081365
+chr20	18209139	18210134
+chr20	20296014	20296330
+chr20	20320339	20320519
+chr20	20337285	20337624
+chr20	20354912	20355435
+chr20	20356530	20357810
+chr20	21120298	21120461
+chr20	21721451	21721646
+chr20	22082266	22083905
+chr20	23155578	23155857
+chr20	23560939	23561098
+chr20	24408073	24408820
+chr20	24682066	24682125
+chr20	25781790	25781791
+chr20	32723044	32723045
+chr20	34235898	34235981
+chr20	35539212	35539582
+chr20	35580686	35580756
+chr20	37361785	37361886
+chr20	38123799	38124003
+chr20	38463997	38464344
+chr20	41196370	41196495
+chr20	41257714	41258003
+chr20	44764150	44764203
+chr20	45600655	45600695
+chr20	48449794	48450385
+chr20	49834182	49834469
+chr20	50775646	50775832
+chr20	51953819	51953820
+chr20	53204099	53204252
+chr20	55624808	55625652
+chr20	55627638	55628305
+chr20	55944272	55945175
+chr20	56280541	56281913
+chr20	57090868	57091166
+chr20	57110450	57110593
+chr20	57190256	57190428
+chr20	57350856	57350920
+chr20	57949001	57949346
+chr20	59384366	59384743
+chr20	60314443	60314711
+chr20	60703005	60703087
+chr20	61100921	61102405
+chr20	61201822	61202242
+chr20	61282925	61283479
+chr20	61289662	61290273
+chr20	61329345	61329441
+chr20	61562109	61562252
+chr20	61744401	61744592
+chr20	61783958	61784698
+chr20	62057602	62058768
+chr20	62270413	62270827
+chr20	62321396	62321730
+chr20	62349641	62349826
+chr20	62360410	62360602
+chr20	62830650	62830697
+chr20	62875241	62875404
+chr20	63028066	63029030
+chr20	63049093	63049159
+chr20	63154687	63154921
+chr20	63167473	63167564
+chr20	63221509	63221721
+chr20	63372214	63372400
+chr20	63491957	63492390
+chr20	63535751	63536002
+chr20	63559415	63559719
+chr20	63641847	63642015
+chr20	63693449	63693732
+chr20	63770936	63771014
+chr20	63948594	63948653
+chr20	63964805	63966113
+chr20	64065882	64065883
+chr20	64090733	64091007
+chr20	64097039	64097040
+chr20	64125360	64127875
+chr20	64131913	64133856
+chr20	64134990	64135308
+chr20	64173438	64176330
\ No newline at end of file
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
new file mode 100644
index 00000000..1bf37b27
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi
new file mode 100644
index 00000000..ebacc167
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fn.vcf.gz.tbi differ
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
new file mode 100644
index 00000000..6f125f07
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi
new file mode 100644
index 00000000..a440ae4b
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/fp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/log.txt b/repo_utils/answer_key/refine/refine_output_two/log.txt
new file mode 100644
index 00000000..f9c2859f
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/log.txt
@@ -0,0 +1,86 @@
+2023-12-19 15:34:01,502 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:34:01,504 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_two
+2023-12-19 15:34:01,505 [INFO] Params:
+{
+    "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz",
+    "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz",
+    "output": "test_results/refine_output_two",
+    "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed",
+    "extend": 0,
+    "debug": false,
+    "reference": null,
+    "refdist": 500,
+    "pctseq": 0.7,
+    "minhaplen": 50,
+    "pctsize": 0.7,
+    "pctovl": 0.0,
+    "typeignore": false,
+    "chunksize": 1000,
+    "bSample": "syndip",
+    "cSample": "HG002",
+    "dup_to_ins": false,
+    "sizemin": 5,
+    "sizefilt": 5,
+    "sizemax": 50000,
+    "passonly": false,
+    "no_ref": false,
+    "pick": "single",
+    "check_monref": true,
+    "check_multi": true
+}
+2023-12-19 15:34:01,573 [INFO] Including 225 bed regions
+2023-12-19 15:34:03,210 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
+2023-12-19 15:34:03,212 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
+2023-12-19 15:34:03,413 [INFO] Stats: {
+    "TP-base": 387,
+    "TP-comp": 387,
+    "FP": 64,
+    "FN": 200,
+    "precision": 0.8580931263858093,
+    "recall": 0.6592844974446337,
+    "f1": 0.745664739884393,
+    "base cnt": 587,
+    "comp cnt": 451,
+    "TP-comp_TP-gt": 382,
+    "TP-comp_FP-gt": 5,
+    "TP-base_TP-gt": 382,
+    "TP-base_FP-gt": 5,
+    "gt_concordance": 0.9870801033591732,
+    "gt_matrix": {
+        "(1, 0)": {
+            "(0, 1)": 203,
+            "(1, 0)": 13,
+            "(1, 1)": 1
+        },
+        "(0, 1)": {
+            "(1, 0)": 146,
+            "(0, 1)": 11
+        },
+        "(1, 1)": {
+            "(1, 1)": 9,
+            "(1, 0)": 2,
+            "(0, 1)": 2
+        }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 500.5166001608595,
+            "FP": 39.91689974069595,
+            "FN": 87.50939983222634,
+            "precision": 0.9261391091633528,
+            "recall": 0.8511810705083529,
+            "f1": 0.88707942147253,
+            "total": 604
+        },
+        "size": {
+            "TP": 485.1211999114603,
+            "FP": 44.722199864685535,
+            "FN": 102.43430008925498,
+            "precision": 0.9155935510689002,
+            "recall": 0.8256602140748741,
+            "f1": 0.8683044166382059,
+            "total": 604
+        }
+    }
+}
+2023-12-19 15:34:03,415 [INFO] Finished bench
diff --git a/repo_utils/answer_key/refine/refine_output_two/params.json b/repo_utils/answer_key/refine/refine_output_two/params.json
new file mode 100644
index 00000000..596718ee
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/params.json
@@ -0,0 +1 @@
+{"base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", "output": "test_results/refine_output_two", "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz
new file mode 100644
index 00000000..e132884d
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi
new file mode 100644
index 00000000..47ccbd36
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/candidate.refine.bed b/repo_utils/answer_key/refine/refine_output_two/phab_bench/candidate.refine.bed
new file mode 100644
index 00000000..1d31809d
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/candidate.refine.bed
@@ -0,0 +1,2 @@
+chr20	5040476	5040477
+chr20	32723044	32723045
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz
new file mode 100644
index 00000000..fe8f9b3e
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi
new file mode 100644
index 00000000..426f818b
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fn.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz
new file mode 100644
index 00000000..9f8ea569
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi
new file mode 100644
index 00000000..a74137fb
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/fp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json
new file mode 100644
index 00000000..4023be31
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json
@@ -0,0 +1 @@
+{"base": "test_results/refine_output_two/phab.output.vcf.gz", "comp": "test_results/refine_output_two/phab.output.vcf.gz", "output": "test_results/refine_output_two/phab_bench", "includebed": "/tmp/rbha7u9j.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json
new file mode 100644
index 00000000..8d850191
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json
@@ -0,0 +1,47 @@
+{
+    "TP-base": 263,
+    "TP-comp": 263,
+    "FP": 2,
+    "FN": 1,
+    "precision": 0.9924528301886792,
+    "recall": 0.9962121212121212,
+    "f1": 0.9943289224952742,
+    "base cnt": 264,
+    "comp cnt": 265,
+    "TP-comp_TP-gt": 263,
+    "TP-comp_FP-gt": 0,
+    "TP-base_TP-gt": 263,
+    "TP-base_FP-gt": 0,
+    "gt_concordance": 1.0,
+    "gt_matrix": {
+        "(0, 1)": {
+            "(1, 0)": 106
+        },
+        "(1, 0)": {
+            "(0, 1)": 112
+        },
+        "(1, 1)": {
+            "(1, 1)": 45
+        }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 262.9908000230789,
+            "FP": 2.0091999769210815,
+            "FN": 1.0091999769210815,
+            "precision": 0.9924181132946375,
+            "recall": 0.9961772728146929,
+            "f1": 0.9942941399738333,
+            "total": 266
+        },
+        "size": {
+            "TP": 263.0,
+            "FP": 2.0,
+            "FN": 1.0,
+            "precision": 0.9924528301886792,
+            "recall": 0.9962121212121212,
+            "f1": 0.9943289224952742,
+            "total": 266
+        }
+    }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000..08484ee2
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi
new file mode 100644
index 00000000..cc1fb34c
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi differ
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
new file mode 100644
index 00000000..58afeef9
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi
new file mode 100644
index 00000000..cc1fb34c
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.log.txt b/repo_utils/answer_key/refine/refine_output_two/refine.log.txt
new file mode 100644
index 00000000..885798db
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.log.txt
@@ -0,0 +1,28 @@
+2023-12-19 15:34:05,536 [INFO] Truvari v4.2.0rc1
+2023-12-19 15:34:05,537 [INFO] Command /data/truvari/__main__.py refine -u -U -r repo_utils/test_files/refine_data/h2_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_two
+2023-12-19 15:34:05,539 [INFO] Params:
+{
+    "benchdir": "test_results/refine_output_two",
+    "reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
+    "regions": "repo_utils/test_files/refine_data/h2_hc_tr_hg002.bed",
+    "use_original_vcfs": true,
+    "use_region_coords": true,
+    "recount": false,
+    "threads": 4,
+    "align": "mafft",
+    "mafft_params": "--auto --thread 1",
+    "debug": false
+}
+2023-12-19 15:34:05,540 [INFO] Setting up regions
+2023-12-19 15:34:05,618 [INFO] 247 --regions reduced to 129 after intersecting with 225 from --includebed
+2023-12-19 15:34:06,241 [INFO] 52 regions to be refined
+2023-12-19 15:34:06,275 [INFO] Preparing regions
+2023-12-19 15:34:06,283 [INFO] Extracting haplotypes
+2023-12-19 15:34:06,821 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:34:06,823 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
+2023-12-19 15:34:06,859 [INFO] Harmonizing variants
+2023-12-19 15:34:08,877 [INFO] Running bench
+2023-12-19 15:34:08,927 [INFO] Including 52 bed regions
+2023-12-19 15:34:09,801 [INFO] Zipped 2598 variants Counter({'base': 1299, 'comp': 1299})
+2023-12-19 15:34:09,802 [INFO] 53 chunks of 2598 variants Counter({'__filtered': 2069, 'comp': 265, 'base': 264})
+2023-12-19 15:34:10,338 [INFO] Finished refine
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
index de10db40..2125f6d6 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 118,
-    "TN": 3,
-    "FP": 7,
+    "TP": 121,
+    "TN": 2,
+    "FP": 5,
     "FN": 1,
-    "base P": 121,
-    "base N": 8,
+    "base P": 122,
+    "base N": 7,
     "comp P": 126,
     "comp N": 3,
-    "PPV": 0.9365079365079365,
-    "TPR": 0.9752066115702479,
-    "TNR": 0.375,
-    "NPV": 1.0,
-    "ACC": 0.937984496124031,
-    "BA": 0.6751033057851239,
-    "F1": 0.9554655870445344,
+    "PPV": 0.9603174603174603,
+    "TPR": 0.9918032786885246,
+    "TNR": 0.2857142857142857,
+    "NPV": 0.6666666666666666,
+    "ACC": 0.9534883720930233,
+    "BA": 0.6387587822014051,
+    "F1": 0.9758064516129032,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
index 1d4dd76e..fc8fd4c9 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
@@ -33,13 +33,13 @@ chr20	22882702	22882830	2	2	0	0	False	2	2	0	0	TP
 chr20	23155504	23155975	3	3	2	2	True	5	5	0	0	TP
 chr20	23267965	23268087	2	2	0	0	False	2	2	0	0	TP
 chr20	23942431	23942955	1	1	0	0	False	1	1	0	0	TP
-chr20	24681988	24682277	2	2	1	0	True	1	1	0	1	FP
+chr20	24681988	24682277	2	2	1	0	True	2	2	0	0	TP
 chr20	24836081	24836384	2	2	0	0	False	2	2	0	0	TP
 chr20	24956961	24957198	2	2	0	0	False	2	2	0	0	TP
 chr20	25067059	25068112	3	3	0	0	False	3	3	0	0	TP
 chr20	25561369	25562321	2	2	0	0	False	2	2	0	0	TP
 chr20	31689079	31689527	2	2	0	0	False	2	2	0	0	TP
-chr20	32722424	32723212	0	0	1	0	True	0	0	0	0	TN
+chr20	32722424	32723212	0	0	1	0	True	0	0	1	0	FN
 chr20	32723469	32724637	0	0	0	0	False	0	0	0	0	TN
 chr20	32724927	32724999	0	0	0	0	False	0	0	0	0	TN
 chr20	34205619	34205960	1	1	0	0	False	1	1	0	0	TP
@@ -97,7 +97,7 @@ chr20	62830612	62830838	2	2	1	1	True	2	2	0	0	TP
 chr20	62875172	62875556	2	2	3	0	True	3	3	0	0	TP
 chr20	62986310	62986805	2	2	0	0	False	2	2	0	0	TP
 chr20	63027997	63028166	2	2	1	0	True	4	4	0	0	TP
-chr20	63028876	63029402	2	2	0	1	True	1	1	0	1	FP
+chr20	63028876	63029402	2	2	0	1	True	2	2	0	0	TP
 chr20	63049033	63049412	3	3	1	0	True	2	2	0	0	TP
 chr20	63068409	63068799	2	2	0	0	False	2	2	0	0	TP
 chr20	63103249	63103492	1	1	0	0	False	1	1	0	0	TP
@@ -125,6 +125,6 @@ chr20	64090704	64091389	0	0	0	2	False	0	0	0	2	FP
 chr20	64096658	64097164	0	0	0	2	False	0	0	0	2	FP
 chr20	64125109	64127974	3	3	3	0	True	12	12	0	0	TP
 chr20	64131804	64133955	5	5	8	1	True	24	24	0	0	TP
-chr20	64134883	64136386	3	3	1	0	True	4	4	1	0	FN
-chr20	64173409	64176529	4	4	7	3	True	18	18	0	0	TP
+chr20	64134883	64136386	3	3	1	0	True	4	4	0	0	TP
+chr20	64173409	64176529	4	4	7	3	True	17	17	0	0	TP
 chr20	64233048	64233545	2	2	0	0	False	2	2	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
index 6a256452..24067482 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 405,
-    "TP-comp": 405,
-    "FP": 12,
+    "TP-base": 406,
+    "TP-comp": 406,
+    "FP": 10,
     "FN": 1,
-    "precision": 0.9712230215827338,
-    "recall": 0.9975369458128078,
-    "f1": 0.9842041312272175,
-    "base cnt": 406,
-    "comp cnt": 417
+    "precision": 0.9759615384615384,
+    "recall": 0.9975429975429976,
+    "f1": 0.9866342648845686,
+    "base cnt": 407,
+    "comp cnt": 416
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/summary.json b/repo_utils/answer_key/refine/refine_output_two/summary.json
new file mode 100644
index 00000000..7c012dba
--- /dev/null
+++ b/repo_utils/answer_key/refine/refine_output_two/summary.json
@@ -0,0 +1,52 @@
+{
+    "TP-base": 387,
+    "TP-comp": 387,
+    "FP": 64,
+    "FN": 200,
+    "precision": 0.8580931263858093,
+    "recall": 0.6592844974446337,
+    "f1": 0.745664739884393,
+    "base cnt": 587,
+    "comp cnt": 451,
+    "TP-comp_TP-gt": 382,
+    "TP-comp_FP-gt": 5,
+    "TP-base_TP-gt": 382,
+    "TP-base_FP-gt": 5,
+    "gt_concordance": 0.9870801033591732,
+    "gt_matrix": {
+        "(1, 0)": {
+            "(0, 1)": 203,
+            "(1, 0)": 13,
+            "(1, 1)": 1
+        },
+        "(0, 1)": {
+            "(1, 0)": 146,
+            "(0, 1)": 11
+        },
+        "(1, 1)": {
+            "(1, 1)": 9,
+            "(1, 0)": 2,
+            "(0, 1)": 2
+        }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 500.5166001608595,
+            "FP": 39.91689974069595,
+            "FN": 87.50939983222634,
+            "precision": 0.9261391091633528,
+            "recall": 0.8511810705083529,
+            "f1": 0.88707942147253,
+            "total": 604
+        },
+        "size": {
+            "TP": 485.1211999114603,
+            "FP": 44.722199864685535,
+            "FN": 102.43430008925498,
+            "precision": 0.9155935510689002,
+            "recall": 0.8256602140748741,
+            "f1": 0.8683044166382059,
+            "total": 604
+        }
+    }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000..22990202
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi
new file mode 100644
index 00000000..8e71cb40
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-base.vcf.gz.tbi differ
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
new file mode 100644
index 00000000..58ac980f
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz differ
diff --git a/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi
new file mode 100644
index 00000000..3e2f5910
Binary files /dev/null and b/repo_utils/answer_key/refine/refine_output_two/tp-comp.vcf.gz.tbi differ
diff --git a/truvari/phab.py b/truvari/phab.py
index 568cb36d..a8b8186b 100644
--- a/truvari/phab.py
+++ b/truvari/phab.py
@@ -93,6 +93,7 @@ def incorporate(consensus_sequence, entry, correction):
     consensus_sequence[position:position + ref_len] = list(entry.alts[0])
     return correction + (alt_len - ref_len)
 
+
 def make_consensus(data, ref_fn):
     """
     Creates consensus sequence from variants
@@ -120,11 +121,11 @@ def make_consensus(data, ref_fn):
                 # Checks - doesn't overlap previous position
                 correction[1] = incorporate(haps[1], entry, correction[1])
         # turn into fasta.
-        ret[ref] = f">{o_samp}_1_{ref}\n{''.join(haps[0])}\n>{o_samp}_2_{ref}\n{''.join(haps[1])}\n".encode()
+        ret[ref] = f">{o_samp}_1_{ref}\n{''.join(haps[0])}\n>{o_samp}_2_{ref}\n{''.join(haps[1])}\n".encode(
+        )
     return ret
 
 
-
 def make_haplotype_jobs(base_vcf, bSamples=None, comp_vcf=None, cSamples=None, prefix_comp=False):
     """
     Sets up sample parameters for extract haplotypes
@@ -173,22 +174,6 @@ def fasta_reader(fa_str, name_entries=True):
     yield cur_name, cur_entry.read()
 
 
-def extract_haplotypes(data, ref_fn):
-    """
-    Deprecated - bcftools consensus isn't great
-    Given a data tuple of VCF, sample name, and prefix bool
-    Call bcftools consensus
-    Returns list of tuples [location, fastaentry] for every haplotype,
-    so locations are duplicated
-    """
-    vcf_fn, sample, prefix, hap = data
-    prefix = 'p:' if prefix else ''
-    cmd = (f"--sample {sample} --prefix {prefix}{sample}_{hap}_ "
-           f"-H{hap} -f {ref_fn} {vcf_fn}").split(' ')
-    # Can't return generator from process
-    return list(fasta_reader(bcftools.consensus(*cmd)))
-
-
 def collect_haplotypes(ref_haps_fn, hap_jobs, threads):
     """
     Calls extract haplotypes for every hap_job