Repository: bioforensics/MicroHapDB (language: python)

Issue:
Issue with detail report for mh06WL-017.v1
## Bug description

Error when running `microhapdb marker mh06WL-017.v1 --format=detail`.


## Observed behavior

```
$ microhapdb marker mh06WL-017.v1 --format=detail
Traceback (most recent call last):
  File "/Users/daniel.standage/anaconda3/envs/microhapdb/bin/microhapdb", line 33, in <module>
    sys.exit(load_entry_point('microhapdb', 'console_scripts', 'microhapdb')())
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/cli/__init__.py", line 67, in main
    mainmethod(args)
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/cli/marker.py", line 29, in main
    display(
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/cli/marker.py", line 87, in display
    print(marker.detail)
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/marker.py", line 238, in detail
    self.print_detail_targetseq(output)
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/marker.py", line 294, in print_detail_targetseq
    self.print_detail_targetseq_alleles(blocks, out)  # Row 3+: alleles
  File "/Users/daniel.standage/Software/MicroHapDB/microhapdb/marker.py", line 348, in print_detail_targetseq_alleles
    allele=allelevars[n], length=self.variant_lengths[n]
IndexError: list index out of range
```


## Expected behavior

A properly formatted marker detail report.


## Technical specs

- Which version of MicroHapDB are you using? (`microhapdb --version`): MicroHapDB v0.10+3.g62caacb.dirty
- Which version of Python are you running? (`python --version`): Python 3.9.13
- Which operating system (Windows, Mac, Linux) and version (Windows 10, Mac OS X Catalina, Ubuntu 18.04) are you running? MacOS Ventura 13.6



Discussion / hints:

Fix patch:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0aa690fa..546691e6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Changed
 - Merged RSIDs resolved during database build now propagated to the final marker definition (see #149).
 
+### Fixed
+- Added manual and automated fixes to ensure frequencies are formatted correcly and matche to the correct marker definition (see #150).
+
 
 ## [0.10.1] 2023-10-13
 
diff --git a/dbbuild/build-summary.txt b/dbbuild/build-summary.txt
index ff6ad5ab..6214cee1 100644
--- a/dbbuild/build-summary.txt
+++ b/dbbuild/build-summary.txt
@@ -3034,7 +3034,7 @@ Marker mh11KK-040 as defined in Staadig2021 was defined previously and is redund
   - 59 marker definitions based on 658 SNPs
 [Byrska-Bishop2022]
   - 31 population samples
-  - frequencies for 59232 distinct haplotypes in 31 populations; 856064 total frequencies
+  - frequencies for 59233 distinct haplotypes in 31 populations; 856067 total frequencies
 [Fan2022]
   - 22 marker definitions based on 338 SNPs and 25 indels
 [Yu2022G1]
diff --git a/dbbuild/build.py b/dbbuild/build.py
index 89931cd5..af1a69b2 100755
--- a/dbbuild/build.py
+++ b/dbbuild/build.py
@@ -30,9 +30,9 @@ def main(
     index.update_marker_names()
     index.markers.to_csv("marker.csv", index=False)
     index.indels.to_csv("indels.csv", index=False)
-    index.frequencies.to_csv(
-        "frequency.csv.gz", index=False, float_format="%.5f", compression="gzip"
-    )
+    frequencies = index.frequencies
+    frequencies = cleanup_frequencies(frequencies)
+    frequencies.to_csv("frequency.csv.gz", index=False, float_format="%.5f", compression="gzip")
     index.populations.to_csv("population.csv", index=False)
     index.merges.to_csv("merged.csv", index=False)
     repeats = flag_repeats(Path(rmsk_path) / "rmsk.txt.gz", "marker.csv", delta=25)
@@ -60,6 +60,22 @@ def validate_paths(dbsnp_path, rmsk_path, chain_path):
         raise FileNotFoundError(",".join(missing))
 
 
+def cleanup_frequencies(freq):
+    freq["NumVars"] = freq.Allele.apply(lambda x: x.count("|") + 1)
+    freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Kidd2018"), "Marker"] = "mh01NH-01.v2"
+    freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Turchi2019"), "Marker"] = "mh01NH-01.v2"
+    freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Gandotra2020"), "Marker"] = "mh01NH-01.v2"
+    freq.loc[(freq.Marker == "mh01NK-001") & (freq.Source == "Staadig2021"), "Marker"] = "mh01NH-01.v1"
+    freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Kidd2018") & (freq.NumVars == 3), "Marker"] = "mh05KK-023.v1"
+    freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Kidd2018") & (freq.NumVars == 4), "Marker"] = "mh05KK-023.v2"
+    freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Turchi2019"), "Marker"] = "mh05KK-023.v1"
+    freq.loc[(freq.Marker.str.startswith(("mh05KK-023", "mh05KK-020"))) & (freq.Source == "Gandotra2020"), "Marker"] = "mh05KK-023.v3"
+    freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 3), "Marker"] = "mh05KK-120.v1"
+    freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 4), "Marker"] = "mh05KK-120.v2"
+    freq = freq.drop(columns="NumVars")
+    return freq
+
+
 def get_parser():
     parser = ArgumentParser(description="MicroHapDB database build procedure")
     parser.add_argument("dbsnp_path")
diff --git a/dbbuild/frequency.csv.gz b/dbbuild/frequency.csv.gz
index 906ce9f0..4aeecab8 100644
Binary files a/dbbuild/frequency.csv.gz and b/dbbuild/frequency.csv.gz differ
diff --git a/dbbuild/marker-aes.csv b/dbbuild/marker-aes.csv
index d765b5cb..2450003d 100644
--- a/dbbuild/marker-aes.csv
+++ b/dbbuild/marker-aes.csv
@@ -36048,8 +36048,8 @@ mh06WL-017.v1,MXL,6.983
 mh06WL-017.v1,PEL,7.292
 mh06WL-017.v1,PJL,6.547
 mh06WL-017.v1,PUR,7.729
-mh06WL-017.v1,SAS,8.805
-mh06WL-017.v1,STU,10.080
+mh06WL-017.v1,SAS,8.806
+mh06WL-017.v1,STU,10.085
 mh06WL-017.v1,TSI,8.339
 mh06WL-017.v1,YRI,6.634
 mh06WL-017.v2,1KGP,8.679
diff --git a/dbbuild/marker.csv b/dbbuild/marker.csv
index de0a12df..164d7b87 100644
--- a/dbbuild/marker.csv
+++ b/dbbuild/marker.csv
@@ -1109,7 +1109,7 @@ mh06SCUZJ-0278537,4,130,chr6,32588674,32588803,32588674;32588684;32588765;325888
 mh06SHY-003,12,91,chr6,32605762,32605852,32605762;32605766;32605777;32605783;32605785;32605788;32605797;32605821;32605825;32605844;32605851;32605852,32573539;32573543;32573554;32573560;32573562;32573565;32573574;32573598;32573602;32573621;32573628;32573629,rs602427;rs9270967;rs9270968;rs9270969;rs602457;rs573809619;rs9270970;rs9270971;rs2760993;rs9270972;rs144123929;rs602875,Wu2021
 mh06WL-050,27,300,chr6,32661208,32661507,32661208;32661214;32661215;32661219;32661221;32661238;32661245;32661250;32661255;32661269;32661287;32661289;32661297;32661310;32661314;32661332;32661333;32661334;32661335;32661462;32661463;32661482;32661490;32661492;32661504;32661505;32661507,32628985;32628991;32628992;32628996;32628998;32629015;32629022;32629027;32629032;32629046;32629064;32629066;32629074;32629087;32629091;32629109;32629110;32629111;32629112;32629239;32629240;32629259;32629267;32629269;32629281;32629282;32629284,rs28724236;rs117369774;rs117656997;rs9273560;rs9273561;rs281864341;rs281864337;rs41270893;rs73729446;rs28724237;rs9273584;rs28724238;rs9273588;rs117626117;rs9273595;rs281864289;rs9273608;rs281864287;rs9273609;rs559673115;rs281864275;rs3828786;rs199987570;rs9273685;rs9273695;rs9273696;rs114262759,Yu2022G3
 mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219,Yu2022G4
-mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663288;32663293;32663298;32663302;32663303;32663327;32663332;32663336;32663342;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631065;32631070;32631075;32631079;32631080;32631104;32631109;32631113;32631119;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs17843723;rs41270932;rs9274222;rs72844333;rs200098349;rs74222206;rs281863378;rs9274225;rs41270933;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
+mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663293;32663298;32663302;32663303;32663309;32663327;32663332;32663336;32663342;32663345;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs41270932;rs9274222;rs72844333;rs200098349;rs17843724;rs74222206;rs281863378;rs9274225;rs41270933;rs17613622;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
 mh06LV-09,14,193,chr6,33056355,33056547,33056355;33056360;33056389;33056401;33056412;33056447;33056452;33056458;33056481;33056496;33056522;33056532;33056540;33056547,33024132;33024137;33024166;33024178;33024189;33024224;33024229;33024235;33024258;33024273;33024299;33024309;33024317;33024324,rs412735;rs570318069;rs449635;rs114484337;rs150884041;rs6457707;rs396638;rs6457708;rs12200756;rs435549;rs3130593;rs3130184;rs3130185;rs3130594,Voskoboinik2018
 mh06WL-070,5,85,chr6,33893893,33893977,33893893;33893902;33893916;33893934;33893977,33861670;33861679;33861693;33861711;33861754,rs3800333;rs2031377;rs3800335;rs2031378;rs3800337,Yu2022G1
 mh06WL-075,5,134,chr6,36734497,36734630,36734497;36734507;36734602;36734610;36734630,36702274;36702284;36702379;36702387;36702407,rs236453;rs236452;rs236451;rs77394127;rs236450,Yu2022G1
diff --git a/dbbuild/sources/byrskabishop2022/frequency.csv b/dbbuild/sources/byrskabishop2022/frequency.csv
index 6fdfc442..19e43452 100644
--- a/dbbuild/sources/byrskabishop2022/frequency.csv
+++ b/dbbuild/sources/byrskabishop2022/frequency.csv
@@ -330495,537 +330495,540 @@ mh06WL-014.v2,YRI,C|G|G|A|C,0.19421
 mh06WL-014.v2,YRI,C|G|G|A|T,0.04545
 mh06WL-014.v2,YRI,C|G|G|G|C,0.19835
 mh06WL-014.v2,YRI,C|G|G|G|T,0.07025
-mh06WL-017.v1,1KGP,A|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|T|G,0.00019
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|A|A|C|A|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|G|T|G|T|A,0.00038
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|A|A|C|A|T|T|A|G|C|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.00019
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|A|A|C|T|T|T|A|G|C|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.04407
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|A|A|C|T|T|T|A|G|T|T|G|A|C|T|T|A|A|G|A|C|A|T|G|C|A,0.00019
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|A|A|C|T|T|T|A|G|T|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.03541
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|G|A|C|A|C|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|T|G,0.00019
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|G|T|G|T|A,0.00038
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|G|A|C|T|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|G|T|G|T|A,0.00038
-mh06WL-017.v1,1KGP,A|C|C|G|C|A|G|A|C|T|T|T|A|G|C|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.11875
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|C|A|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|T|G,0.08333
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|C|A|A|C|T|G|A|C|T|T|G|A|A|A|C|A|T|G|C|A,0.03637
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|C|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|T|G,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|A|C|T|G|A|C|T|T|G|A|A|A|C|A|T|G|C|A,0.13433
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|C|A|G|C|T|C|G|A|A|A|T|A|T|G|T|G,0.06928
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|C|C|G|A|A|A|C|A|T|G|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|C|C|G|A|A|A|T|G|T|G|T|A,0.04426
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|A|T|G|T|G,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|G|T|G|T|A,0.12760
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.00423
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|T|G|A|A|A|C|G|T|G|T|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|T|G|A|A|A|T|G|T|G|T|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|T|G|A|A|T|T|A|C|A|C|A,0.00038
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|T|T|G|T|A|A|T|G|T|G|C|G,0.00154
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|A|G|T|T|G|A|C|T|T|A|A|G|A|T|A|T|G|C|A,0.00038
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|G|G|C|T|G|A|T|T|T|G|A|A|T|T|A|C|A|C|A,0.00192
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|C|A|T|T|G|G|C|T|G|G|T|T|T|G|A|A|T|T|A|C|A|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|A|G|C|T|G|A|C|C|C|G|A|A|A|T|G|T|G|T|A,0.00038
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|A|G|C|T|G|A|C|T|C|G|A|A|A|T|G|T|G|T|A,0.00096
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|T|G|A|A|A|C|A|T|G|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|T|G|A|A|T|C|A|C|A|C|A,0.00019
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|T|G|A|A|T|T|A|C|A|C|A,0.14550
-mh06WL-017.v1,1KGP,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|T|G|A|A|T|T|A|C|A|C|G,0.00038
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+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|A|T|G|T|G,0.00097
+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.17539
+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|G,0.00097
+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|T|G|T|G,0.00097
+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|G|C|A|T|T|A|G|C|T|G|A|C|C|G|A|G|A|A|T|G|A|T|G|T|A,0.00097
+mh06WL-017.v1,SAS,G|C|C|A|C|A|G|G|C|A|T|T|A|G|C|T|G|A|T|T|G|T|G|A|A|T|G|A|T|G|C|G,0.18120
+mh06WL-017.v1,SAS,G|C|T|A|C|A|A|A|C|T|T|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.00097
+mh06WL-017.v1,SAS,G|C|T|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.09109
+mh06WL-017.v1,SAS,G|C|T|A|C|A|G|A|C|T|T|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.00194
+mh06WL-017.v1,STU,A|C|C|G|C|A|A|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.02404
+mh06WL-017.v1,STU,A|C|C|G|C|A|A|A|C|T|T|T|A|G|T|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.09135
+mh06WL-017.v1,STU,A|C|C|G|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|C|G|A|G|A|A|T|G|A|T|G|T|A,0.00481
+mh06WL-017.v1,STU,A|C|C|G|C|A|G|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.07212
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.09615
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|C|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.04808
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|T|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.12500
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.03365
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|C|G|A|G|A|A|T|G|A|T|G|T|A,0.02404
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|C|G|A|G|A|A|T|G|A|T|G|T|A,0.09615
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|T|G|T|G|A|A|T|G|A|T|G|C|G,0.00481
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|A|T|G|T|G,0.00481
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.13942
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|T|G|T|G,0.00481
+mh06WL-017.v1,STU,G|C|C|A|C|A|G|G|C|A|T|T|A|G|C|T|G|A|T|T|G|T|G|A|A|T|G|A|T|G|C|G,0.13462
+mh06WL-017.v1,STU,G|C|T|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.09615
+mh06WL-017.v1,TSI,A|C|C|G|C|A|A|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.04206
+mh06WL-017.v1,TSI,A|C|C|G|C|A|A|A|C|T|T|T|A|G|T|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.04673
+mh06WL-017.v1,TSI,A|C|C|G|C|A|G|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.08879
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.05140
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|C|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.05140
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.13084
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.07477
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|C|G|A|G|A|A|T|G|A|T|G|T|A,0.04673
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|C|G|A|G|A|A|T|G|A|T|G|T|A,0.17290
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.01402
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|C|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.00467
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|T|A|T|T|A|G|C|T|G|A|C|C|G|A|G|A|A|T|G|A|T|G|T|A,0.00467
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|T|A|T|T|A|G|C|T|G|A|T|C|G|A|G|A|A|T|G|A|T|G|T|A,0.00935
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.21495
+mh06WL-017.v1,TSI,G|C|C|A|C|A|G|G|C|A|T|T|A|G|C|T|G|A|T|T|G|T|G|A|A|T|G|A|T|G|C|G,0.00935
+mh06WL-017.v1,TSI,G|C|T|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.03738
+mh06WL-017.v1,YRI,A|C|C|G|C|A|A|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.05372
+mh06WL-017.v1,YRI,A|C|C|G|C|A|A|A|C|T|T|T|A|G|T|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.02066
+mh06WL-017.v1,YRI,A|C|C|G|C|A|G|A|C|T|T|T|A|G|C|T|G|A|T|T|A|A|G|G|A|T|A|A|T|G|C|A,0.11983
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.01240
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|C|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.03719
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|A|A|C|T|G|A|T|T|G|A|G|A|A|C|A|A|T|G|C|A,0.25620
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.09091
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|C|C|G|A|G|A|A|T|G|A|T|G|T|A,0.01653
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|C|G|A|G|A|A|T|G|A|T|G|T|A,0.14876
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|A|G|C|T|G|A|T|T|G|A|G|A|A|T|G|A|T|G|T|A,0.00413
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|C|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.00826
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|A|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.18182
+mh06WL-017.v1,YRI,G|C|C|A|C|A|G|A|T|A|T|T|G|G|C|T|G|G|T|T|G|A|A|A|T|T|A|G|C|A|C|A,0.04545
+mh06WL-017.v1,YRI,G|C|T|A|C|A|G|A|C|A|C|T|A|G|C|C|A|G|T|C|G|A|G|A|A|T|A|A|T|G|T|G,0.00413
 mh06WL-017.v2,1KGP,A|C|C|A|C|A|G|A|C|A|C|T|A|G|C|C,0.00019
 mh06WL-017.v2,1KGP,A|C|C|G|C|A|A|A|C|A|T|T|A|G|C|T,0.00058
 mh06WL-017.v2,1KGP,A|C|C|G|C|A|A|A|C|T|T|T|A|G|C|T,0.04407
diff --git a/dbbuild/sources/byrskabishop2022/haplotypes.csv.gz b/dbbuild/sources/byrskabishop2022/haplotypes.csv.gz
index e9720696..5aac41eb 100644
Binary files a/dbbuild/sources/byrskabishop2022/haplotypes.csv.gz and b/dbbuild/sources/byrskabishop2022/haplotypes.csv.gz differ
diff --git a/dbbuild/sources/byrskabishop2022/marker-aes.csv b/dbbuild/sources/byrskabishop2022/marker-aes.csv
index d765b5cb..2450003d 100644
--- a/dbbuild/sources/byrskabishop2022/marker-aes.csv
+++ b/dbbuild/sources/byrskabishop2022/marker-aes.csv
@@ -36048,8 +36048,8 @@ mh06WL-017.v1,MXL,6.983
 mh06WL-017.v1,PEL,7.292
 mh06WL-017.v1,PJL,6.547
 mh06WL-017.v1,PUR,7.729
-mh06WL-017.v1,SAS,8.805
-mh06WL-017.v1,STU,10.080
+mh06WL-017.v1,SAS,8.806
+mh06WL-017.v1,STU,10.085
 mh06WL-017.v1,TSI,8.339
 mh06WL-017.v1,YRI,6.634
 mh06WL-017.v2,1KGP,8.679
diff --git a/dbbuild/sources/byrskabishop2022/util.py b/dbbuild/sources/byrskabishop2022/util.py
index f5f5506a..4141c633 100644
--- a/dbbuild/sources/byrskabishop2022/util.py
+++ b/dbbuild/sources/byrskabishop2022/util.py
@@ -46,6 +46,9 @@ def __init__(self, vcf, refr_fasta):
 
     def get_haplotypes(self, chrom, positions):
         reference = self.get_reference_haplotype(chrom, positions)
+        if len(reference) != len(positions):
+            message = f"variant count mismatch: {len(reference)} vs {len(positions)}"
+            raise ValueError(message)
         haplotypes = dict()
         for sample in self.samples:
             haplotypes[sample] = (Haplotype(reference), Haplotype(reference))
diff --git a/dbbuild/sources/yu2022g1/README.md b/dbbuild/sources/yu2022g1/README.md
index cb72605b..0ea7100b 100644
--- a/dbbuild/sources/yu2022g1/README.md
+++ b/dbbuild/sources/yu2022g1/README.md
@@ -40,10 +40,12 @@ mh06WL-068b,3,247,chr6,130615104,130615350,130615104;130615240;130615350,1309362
 
 Oddly, the marker mh06WL-069 is defined twice in Group 1, first at the locus chr6:32630944-32631142 and second at the locus chr6:108031328-108031471. The first definition perfectly matches the definition for mh06WL-017 in Group 2, both of which overlap with the marker mh06WL-037 defined in Group 4. The Group 1 definition for mh06WL-069 was updated to use the name mh06WL-017. The label mh06WL-037 ends up getting merged with mh06WL-017 in the final build.
 
+Also, we noted discrepancies between the RSIDs and the GRCh37 positions for the 32-SNP 199 bp definition at this locus. Accordingly, rs58770498 was manually replaced with rs17843724 and rs17843723 with rs17843723 to match the indicated positions in the original published definition for this marker.
+
 ```
 $ grep -e mh06WL-069 -e mh06WL-037 -e mh06WL-017 microhapdb/data/marker.csv
-mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426,Yu2022G4
-mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663288;32663293;32663298;32663302;32663303;32663327;32663332;32663336;32663342;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631065;32631070;32631075;32631079;32631080;32631104;32631109;32631113;32631119;32631129;32631130;32631133;32631142,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs58770498;rs281863382;rs281863378;rs281863375;rs281863371;rs17843723;rs281863364;rs281863363;rs281863362;rs281863357,Yu2022G1;Yu2022G2
+mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219,Yu2022G4
+mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663293;32663298;32663302;32663303;32663309;32663327;32663332;32663336;32663342;32663345;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs41270932;rs9274222;rs72844333;rs200098349;rs17843724;rs74222206;rs281863378;rs9274225;rs41270933;rs17613622;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
 mh06WL-069,3,144,chr6,107710124,107710267,107710124;107710141;107710267,108031328;108031345;108031471,rs9386660;rs539627870;rs2748441,Yu2022G1
 $ grep -e mh06WL-017 -e mh06WL-037 -e mh06WL-069 microhapdb/data/merged.csv 
 mh06WL-037,mh06WL-017
diff --git a/dbbuild/sources/yu2022g1/Yu2022-TableS1.tsv b/dbbuild/sources/yu2022g1/Yu2022-TableS1.tsv
index df916320..4f6793b0 100644
--- a/dbbuild/sources/yu2022g1/Yu2022-TableS1.tsv
+++ b/dbbuild/sources/yu2022g1/Yu2022-TableS1.tsv
@@ -259,7 +259,7 @@ mh05WL-073	172122829;172122833;172122939;172122980	rs7701150;rs78422403;rs772134
 mh05WL-074	165749755;165749891;165749904	rs6876914;rs35855229;rs76228434	4.03
 mh05WL-075	136493820;136493839;136493923;136494011	rs1434664;rs1434665;rs11745960;rs55909424	4.03
 mh05WL-076	29503392;29503454;29503553;29503586	rs1354575;rs182780;rs191312;rs78242558	4.02
-mh06WL-069	32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142	rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs58770498;rs281863382;rs281863378;rs281863375;rs281863371;rs17843723;rs281863364;rs281863363;rs281863362;rs281863357	15.69
+mh06WL-069	32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142	rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs17843724;rs281863382;rs281863378;rs281863375;rs281863371;rs17613622;rs281863364;rs281863363;rs281863362;rs281863357	15.69
 mh06WL-018	168961083;168961168;168961183;168961185;168961192;168961205;168961251;168961252;168961257	rs34170156;rs12526829;rs10945514;rs200538603;rs57987480;rs55685832;rs10945516;rs13215061;rs372903846	14.09
 mh06WL-019	786166;786213;786222;786223	rs12055421;rs12055469;rs9505149;rs9392876	10.87
 mh06WL-066	31274441;31274449;31274513;31274555;31274580;31274582;31274586;31274619;31274630;31274634	rs9468942;rs35647108;rs6931873;rs10484554;rs184149624;rs9468944;rs561074738;rs9264944;rs118169956;rs9264946	7.50
diff --git a/dbbuild/sources/yu2022g1/marker.csv b/dbbuild/sources/yu2022g1/marker.csv
index 105fe871..93f5d687 100644
--- a/dbbuild/sources/yu2022g1/marker.csv
+++ b/dbbuild/sources/yu2022g1/marker.csv
@@ -259,7 +259,7 @@ mh05WL-073,,4,,chr5,,rs7701150;rs78422403;rs7721347;rs7701713
 mh05WL-074,,3,,chr5,,rs6876914;rs35855229;rs76228434
 mh05WL-075,,4,,chr5,,rs1434664;rs1434665;rs11745960;rs55909424
 mh05WL-076,,4,,chr5,,rs1354575;rs182780;rs191312;rs78242558
-mh06WL-017,,32,,chr6,,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs58770498;rs281863382;rs281863378;rs281863375;rs281863371;rs17843723;rs281863364;rs281863363;rs281863362;rs281863357
+mh06WL-017,,32,,chr6,,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs17843724;rs281863382;rs281863378;rs281863375;rs281863371;rs17613622;rs281863364;rs281863363;rs281863362;rs281863357
 mh06WL-018,,9,,chr6,,rs34170156;rs12526829;rs10945514;rs200538603;rs57987480;rs55685832;rs10945516;rs13215061;rs372903846
 mh06WL-019,,4,,chr6,,rs12055421;rs12055469;rs9505149;rs9392876
 mh06WL-066a,,10,,chr6,,rs9468942;rs35647108;rs6931873;rs10484554;rs184149624;rs9468944;rs561074738;rs9264944;rs118169956;rs9264946
diff --git a/dbbuild/sources/yu2022g2/Yu2022-TableS2.tsv b/dbbuild/sources/yu2022g2/Yu2022-TableS2.tsv
index d8427b21..687d3f1d 100755
--- a/dbbuild/sources/yu2022g2/Yu2022-TableS2.tsv
+++ b/dbbuild/sources/yu2022g2/Yu2022-TableS2.tsv
@@ -112,7 +112,7 @@ mh05WL-030	56292990;56293009;56293054;56293077;56293149	rs57258507;rs17732378;rs
 mh05WL-031	146337694;146337725;146337743;146337873	rs7726431;rs143876253;rs13170982;rs17105785	4.20		4	180
 mh05WL-013	62073698;62073771;62073783;62073792;62073794;62073834	rs7715472;rs2642778;rs2591790;rs2591791;rs2642779;rs2642780	4.16		6	137
 mh05WL-033	141129129;141129204;141129208;141129248	rs3797057;rs32946;rs117055966;rs32945	4.13		4	120
-mh06WL-017	32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142	rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs58770498;rs281863382;rs281863378;rs281863375;rs281863371;rs17843723;rs281863364;rs281863363;rs281863362;rs281863357	15.69	6.43	32	199
+mh06WL-017	32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142	rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs17843724;rs281863382;rs281863378;rs281863375;rs281863371;rs17613622;rs281863364;rs281863363;rs281863362;rs281863357	15.69	6.43	32	199
 mh06WL-018	168961083;168961168;168961183;168961185;168961192;168961205;168961251;168961252;168961257	rs34170156;rs12526829;rs10945514;rs200538603;rs57987480;rs55685832;rs10945516;rs13215061;rs372903846	14.10		9	175
 mh06WL-019	786166;786213;786222;786223	rs12055421;rs12055469;rs9505149;rs9392876	10.87		4	58
 mh06WL-004	110655384;110655443;110655536;110655552	rs9374163;rs9372250;rs9320324;rs9320325	6.88		4	169
diff --git a/dbbuild/sources/yu2022g2/marker.csv b/dbbuild/sources/yu2022g2/marker.csv
index 5d7fb88a..d7765aa4 100644
--- a/dbbuild/sources/yu2022g2/marker.csv
+++ b/dbbuild/sources/yu2022g2/marker.csv
@@ -112,7 +112,7 @@ mh05WL-030,,5,,chr5,,rs57258507;rs17732378;rs61467430;rs58051462;rs76933101
 mh05WL-031,,4,,chr5,,rs7726431;rs143876253;rs13170982;rs17105785
 mh05WL-013,,6,,chr5,,rs7715472;rs2642778;rs2591790;rs2591791;rs2642779;rs2642780
 mh05WL-033,,4,,chr5,,rs3797057;rs32946;rs117055966;rs32945
-mh06WL-017,,32,,chr6,,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs58770498;rs281863382;rs281863378;rs281863375;rs281863371;rs17843723;rs281863364;rs281863363;rs281863362;rs281863357
+mh06WL-017,,32,,chr6,,rs281863504;rs281863503;rs281863502;rs281863499;rs281863486;rs281863485;rs35986240;rs281863467;rs281863466;rs281863464;rs281863463;rs281863439;rs281863431;rs281863430;rs281863427;rs281863426;rs281863425;rs281863414;rs281863406;rs281863401;rs281863398;rs281863397;rs17843724;rs281863382;rs281863378;rs281863375;rs281863371;rs17613622;rs281863364;rs281863363;rs281863362;rs281863357
 mh06WL-018,,9,,chr6,,rs34170156;rs12526829;rs10945514;rs200538603;rs57987480;rs55685832;rs10945516;rs13215061;rs372903846
 mh06WL-019,,4,,chr6,,rs12055421;rs12055469;rs9505149;rs9392876
 mh06WL-004,,4,,chr6,,rs9374163;rs9372250;rs9320324;rs9320325
diff --git a/microhapdb/data/frequency.csv.gz b/microhapdb/data/frequency.csv.gz
index 906ce9f0..4aeecab8 100644
Binary files a/microhapdb/data/frequency.csv.gz and b/microhapdb/data/frequency.csv.gz differ
diff --git a/microhapdb/data/marker-aes.csv b/microhapdb/data/marker-aes.csv
index d765b5cb..2450003d 100644
--- a/microhapdb/data/marker-aes.csv
+++ b/microhapdb/data/marker-aes.csv
@@ -36048,8 +36048,8 @@ mh06WL-017.v1,MXL,6.983
 mh06WL-017.v1,PEL,7.292
 mh06WL-017.v1,PJL,6.547
 mh06WL-017.v1,PUR,7.729
-mh06WL-017.v1,SAS,8.805
-mh06WL-017.v1,STU,10.080
+mh06WL-017.v1,SAS,8.806
+mh06WL-017.v1,STU,10.085
 mh06WL-017.v1,TSI,8.339
 mh06WL-017.v1,YRI,6.634
 mh06WL-017.v2,1KGP,8.679
diff --git a/microhapdb/data/marker.csv b/microhapdb/data/marker.csv
index de0a12df..164d7b87 100644
--- a/microhapdb/data/marker.csv
+++ b/microhapdb/data/marker.csv
@@ -1109,7 +1109,7 @@ mh06SCUZJ-0278537,4,130,chr6,32588674,32588803,32588674;32588684;32588765;325888
 mh06SHY-003,12,91,chr6,32605762,32605852,32605762;32605766;32605777;32605783;32605785;32605788;32605797;32605821;32605825;32605844;32605851;32605852,32573539;32573543;32573554;32573560;32573562;32573565;32573574;32573598;32573602;32573621;32573628;32573629,rs602427;rs9270967;rs9270968;rs9270969;rs602457;rs573809619;rs9270970;rs9270971;rs2760993;rs9270972;rs144123929;rs602875,Wu2021
 mh06WL-050,27,300,chr6,32661208,32661507,32661208;32661214;32661215;32661219;32661221;32661238;32661245;32661250;32661255;32661269;32661287;32661289;32661297;32661310;32661314;32661332;32661333;32661334;32661335;32661462;32661463;32661482;32661490;32661492;32661504;32661505;32661507,32628985;32628991;32628992;32628996;32628998;32629015;32629022;32629027;32629032;32629046;32629064;32629066;32629074;32629087;32629091;32629109;32629110;32629111;32629112;32629239;32629240;32629259;32629267;32629269;32629281;32629282;32629284,rs28724236;rs117369774;rs117656997;rs9273560;rs9273561;rs281864341;rs281864337;rs41270893;rs73729446;rs28724237;rs9273584;rs28724238;rs9273588;rs117626117;rs9273595;rs281864289;rs9273608;rs281864287;rs9273609;rs559673115;rs281864275;rs3828786;rs199987570;rs9273685;rs9273695;rs9273696;rs114262759,Yu2022G3
 mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219,Yu2022G4
-mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663288;32663293;32663298;32663302;32663303;32663327;32663332;32663336;32663342;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631065;32631070;32631075;32631079;32631080;32631104;32631109;32631113;32631119;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs17843723;rs41270932;rs9274222;rs72844333;rs200098349;rs74222206;rs281863378;rs9274225;rs41270933;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
+mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663293;32663298;32663302;32663303;32663309;32663327;32663332;32663336;32663342;32663345;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs41270932;rs9274222;rs72844333;rs200098349;rs17843724;rs74222206;rs281863378;rs9274225;rs41270933;rs17613622;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
 mh06LV-09,14,193,chr6,33056355,33056547,33056355;33056360;33056389;33056401;33056412;33056447;33056452;33056458;33056481;33056496;33056522;33056532;33056540;33056547,33024132;33024137;33024166;33024178;33024189;33024224;33024229;33024235;33024258;33024273;33024299;33024309;33024317;33024324,rs412735;rs570318069;rs449635;rs114484337;rs150884041;rs6457707;rs396638;rs6457708;rs12200756;rs435549;rs3130593;rs3130184;rs3130185;rs3130594,Voskoboinik2018
 mh06WL-070,5,85,chr6,33893893,33893977,33893893;33893902;33893916;33893934;33893977,33861670;33861679;33861693;33861711;33861754,rs3800333;rs2031377;rs3800335;rs2031378;rs3800337,Yu2022G1
 mh06WL-075,5,134,chr6,36734497,36734630,36734497;36734507;36734602;36734610;36734630,36702274;36702284;36702379;36702387;36702407,rs236453;rs236452;rs236451;rs77394127;rs236450,Yu2022G1
diff --git a/microhapdb/marker.py b/microhapdb/marker.py
index cefe0f97..23dc7737 100644
--- a/microhapdb/marker.py
+++ b/microhapdb/marker.py
@@ -338,6 +338,9 @@ def print_detail_targetseq_sequence(self, blocks, out):
     def print_detail_targetseq_alleles(self, blocks, out):
         for allele in self.alleles:
             allelevars = allele.split("|")
+            if len(allelevars) != len(self.variant_lengths):
+                message = f"num var mismatch ({self.name}): {len(allelevars)} vs {len(self.variant_lengths)}"
+                raise ValueError(message)
             n = -1
             for blocktype, blocklength in blocks:
                 if blocktype == "span":


Test patch:
diff --git a/dbbuild/sources/byrskabishop2022/marker-latest.csv b/dbbuild/sources/byrskabishop2022/marker-latest.csv
index de0a12df..164d7b87 100644
--- a/dbbuild/sources/byrskabishop2022/marker-latest.csv
+++ b/dbbuild/sources/byrskabishop2022/marker-latest.csv
@@ -1109,7 +1109,7 @@ mh06SCUZJ-0278537,4,130,chr6,32588674,32588803,32588674;32588684;32588765;325888
 mh06SHY-003,12,91,chr6,32605762,32605852,32605762;32605766;32605777;32605783;32605785;32605788;32605797;32605821;32605825;32605844;32605851;32605852,32573539;32573543;32573554;32573560;32573562;32573565;32573574;32573598;32573602;32573621;32573628;32573629,rs602427;rs9270967;rs9270968;rs9270969;rs602457;rs573809619;rs9270970;rs9270971;rs2760993;rs9270972;rs144123929;rs602875,Wu2021
 mh06WL-050,27,300,chr6,32661208,32661507,32661208;32661214;32661215;32661219;32661221;32661238;32661245;32661250;32661255;32661269;32661287;32661289;32661297;32661310;32661314;32661332;32661333;32661334;32661335;32661462;32661463;32661482;32661490;32661492;32661504;32661505;32661507,32628985;32628991;32628992;32628996;32628998;32629015;32629022;32629027;32629032;32629046;32629064;32629066;32629074;32629087;32629091;32629109;32629110;32629111;32629112;32629239;32629240;32629259;32629267;32629269;32629281;32629282;32629284,rs28724236;rs117369774;rs117656997;rs9273560;rs9273561;rs281864341;rs281864337;rs41270893;rs73729446;rs28724237;rs9273584;rs28724238;rs9273588;rs117626117;rs9273595;rs281864289;rs9273608;rs281864287;rs9273609;rs559673115;rs281864275;rs3828786;rs199987570;rs9273685;rs9273695;rs9273696;rs114262759,Yu2022G3
 mh06WL-017.v2,16,100,chr6,32663167,32663266,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219,Yu2022G4
-mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663288;32663293;32663298;32663302;32663303;32663327;32663332;32663336;32663342;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631065;32631070;32631075;32631079;32631080;32631104;32631109;32631113;32631119;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs17843723;rs41270932;rs9274222;rs72844333;rs200098349;rs74222206;rs281863378;rs9274225;rs41270933;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
+mh06WL-017.v1,32,199,chr6,32663167,32663365,32663167;32663168;32663169;32663172;32663190;32663191;32663214;32663218;32663219;32663222;32663223;32663252;32663261;32663262;32663265;32663266;32663267;32663281;32663293;32663298;32663302;32663303;32663309;32663327;32663332;32663336;32663342;32663345;32663352;32663353;32663356;32663365,32630944;32630945;32630946;32630949;32630967;32630968;32630991;32630995;32630996;32630999;32631000;32631029;32631038;32631039;32631042;32631043;32631044;32631058;32631070;32631075;32631079;32631080;32631086;32631104;32631109;32631113;32631119;32631122;32631129;32631130;32631133;32631142,rs71542446;rs41270931;rs28724261;rs71542447;rs2854267;rs9274216;rs35986240;rs201930518;rs17613599;rs71542448;rs9274217;rs58770498;rs17613606;rs9274218;rs115495316;rs9274219;rs9274220;rs2856703;rs41270932;rs9274222;rs72844333;rs200098349;rs17843724;rs74222206;rs281863378;rs9274225;rs41270933;rs17613622;rs17613629;rs17613636;rs281863362;rs9274227,Yu2022G1;Yu2022G2
 mh06LV-09,14,193,chr6,33056355,33056547,33056355;33056360;33056389;33056401;33056412;33056447;33056452;33056458;33056481;33056496;33056522;33056532;33056540;33056547,33024132;33024137;33024166;33024178;33024189;33024224;33024229;33024235;33024258;33024273;33024299;33024309;33024317;33024324,rs412735;rs570318069;rs449635;rs114484337;rs150884041;rs6457707;rs396638;rs6457708;rs12200756;rs435549;rs3130593;rs3130184;rs3130185;rs3130594,Voskoboinik2018
 mh06WL-070,5,85,chr6,33893893,33893977,33893893;33893902;33893916;33893934;33893977,33861670;33861679;33861693;33861711;33861754,rs3800333;rs2031377;rs3800335;rs2031378;rs3800337,Yu2022G1
 mh06WL-075,5,134,chr6,36734497,36734630,36734497;36734507;36734602;36734610;36734630,36702274;36702284;36702379;36702387;36702407,rs236453;rs236452;rs236451;rs77394127;rs236450,Yu2022G1
diff --git a/microhapdb/tests/test_cli.py b/microhapdb/tests/test_cli.py
index 0beb54c6..87547ce0 100644
--- a/microhapdb/tests/test_cli.py
+++ b/microhapdb/tests/test_cli.py
@@ -398,7 +398,7 @@ def test_main_marker_bad_code():
         ("--population=SA000009J", "--marker=mh13KK-218.v1", None, 15),
         (None, "--marker=mh13KK-218.v1", "--allele=C|T|C|T", 129),
         (None, "--marker=mh14PK-72639", None, 227),
-        (None, None, None, 944734),
+        (None, None, None, 944737),
     ],
 )
 def test_main_frequency_by_pop(pop, marker, allele, numrows, capsys):
@@ -688,9 +688,9 @@ def test_cli_summarize(capsys):
   - 3053 marker definitions
   - 2413 distinct loci
 [frequencies]
-  - 59772 haplotypes
+  - 59753 haplotypes
   - 125 population groups
-  - 944733 total microhap frequencies
+  - 944736 total microhap frequencies
 """
     print(observed)
     assert observed.strip() == expected.strip()
diff --git a/microhapdb/tests/test_frequency.py b/microhapdb/tests/test_frequency.py
index fb3c7bb7..44a38c28 100644
--- a/microhapdb/tests/test_frequency.py
+++ b/microhapdb/tests/test_frequency.py
@@ -17,7 +17,7 @@
 
 def test_assumptions():
     num_allele_freqs_per_source = [
-        856064,  # Byrska-Bishop2022
+        856067,  # Byrska-Bishop2022
         103,  # Chen2019
         4737,  # Gandotra2020
         33,  # Hiroaki2015
@@ -35,20 +35,20 @@ def test_allele_frequencies():
     >>> f = microhapdb.frequencies
     >>> f[(f.Marker == "mh15CP-003") & (f.Population == "YRI")]
                 Marker Population Allele  Frequency             Source
-    716562  mh15CP-003        YRI  A|A|C    0.02893  Byrska-Bishop2022
-    716563  mh15CP-003        YRI  A|G|A    0.59091  Byrska-Bishop2022
-    716564  mh15CP-003        YRI  A|G|C    0.38017  Byrska-Bishop2022
-    716565  mh15CP-003        YRI  A|G|A    0.57400           Kidd2018
-    716566  mh15CP-003        YRI  A|G|C    0.39800           Kidd2018
-    716567  mh15CP-003        YRI  A|A|C    0.02800           Kidd2018
-    716568  mh15CP-003        YRI  C|G|C    0.00000           Kidd2018
+    716565  mh15CP-003        YRI  A|A|C    0.02893  Byrska-Bishop2022
+    716566  mh15CP-003        YRI  A|G|A    0.59091  Byrska-Bishop2022
+    716567  mh15CP-003        YRI  A|G|C    0.38017  Byrska-Bishop2022
+    716568  mh15CP-003        YRI  A|G|A    0.57400           Kidd2018
+    716569  mh15CP-003        YRI  A|G|C    0.39800           Kidd2018
+    716570  mh15CP-003        YRI  A|A|C    0.02800           Kidd2018
+    716571  mh15CP-003        YRI  C|G|C    0.00000           Kidd2018
     >>> f.query("Marker == 'mh15CP-003' and Allele == 'A|A|C' and Population == 'FIN'")
                 Marker Population Allele  Frequency             Source
-    716439  mh15CP-003        FIN  A|A|C    0.31818  Byrska-Bishop2022
-    716445  mh15CP-003        FIN  A|A|C    0.31800           Kidd2018
+    716442  mh15CP-003        FIN  A|A|C    0.31818  Byrska-Bishop2022
+    716448  mh15CP-003        FIN  A|A|C    0.31800           Kidd2018
     """
     af = microhapdb.frequencies
-    assert af.shape == (944733, 5)
+    assert af.shape == (944736, 5)
     result = af[af.Marker == "mh21KK-315.v1"].Allele.unique()
     assert len(result) == 8
     result = af[(af.Marker == "mh21KK-315.v1") & (af.Allele == "A|C|T")]
@@ -86,3 +86,12 @@ def test_all_sources(marker, pop, allele, frequency):
     result = freq[(freq.Marker == marker) & (freq.Population == pop) & (freq.Allele == allele)]
     assert len(result) == 1
     assert result.Frequency.iloc[0] == pytest.approx(frequency)
+
+
+def test_all_consistent():
+    inconsistent_markers = set()
+    for markerid, table in microhapdb.frequencies.groupby("Marker"):
+        numvars = set([a.count("|") + 1 for a in table.Allele])
+        if len(numvars) > 1:
+            inconsistent_markers.add(markerid)
+    assert len(inconsistent_markers) == 0, sorted(inconsistent_markers)
diff --git a/microhapdb/tests/test_marker.py b/microhapdb/tests/test_marker.py
index 50b1a134..58986169 100644
--- a/microhapdb/tests/test_marker.py
+++ b/microhapdb/tests/test_marker.py
@@ -974,3 +974,46 @@ def test_locus_length():
         loci[marker.locus].markers.append(marker)
     for locus in loci.values():
         assert len(locus.target_seq) <= 610, locus.name
+
+
+def test_mh06WL017v1():
+    subset = microhapdb.markers[microhapdb.markers.Name == "mh06WL-017.v1"]
+    markers = list(Marker.objectify(subset))
+    assert len(markers) == 1
+    marker = markers[0]
+    assert len(marker) == 199
+    print(marker.varrefs)
+    assert marker.varrefs == [
+        "rs71542446",
+        "rs41270931",
+        "rs28724261",
+        "rs71542447",
+        "rs2854267",
+        "rs9274216",
+        "rs35986240",
+        "rs201930518",
+        "rs17613599",
+        "rs71542448",
+        "rs9274217",
+        "rs58770498",
+        "rs17613606",
+        "rs9274218",
+        "rs115495316",
+        "rs9274219",
+        "rs9274220",
+        "rs2856703",
+        "rs41270932",
+        "rs9274222",
+        "rs72844333",
+        "rs200098349",
+        "rs17843724",
+        "rs74222206",
+        "rs281863378",
+        "rs9274225",
+        "rs41270933",
+        "rs17613622",
+        "rs17613629",
+        "rs17613636",
+        "rs281863362",
+        "rs9274227",
+    ]