From 877abbc8cb1d3ff5ff3428f6da2237b4f3b89f9d Mon Sep 17 00:00:00 2001
From: Julia Klugherz <juliaklugherz@gmail.com>
Date: Mon, 28 Oct 2024 17:23:02 -0400
Subject: [PATCH] another pass

---
 hail_search/definitions.py                    |  11 +--
 .../families/WGS/F000002_2.ht/.README.txt.crc | Bin 12 -> 12 bytes
 .../WGS/F000002_2.ht/.metadata.json.gz.crc    | Bin 12 -> 12 bytes
 .../families/WGS/F000002_2.ht/README.txt      |   4 +-
 .../.index.crc                                | Bin
 .../.metadata.json.gz.crc                     | Bin
 .../index                                     | Bin
 .../metadata.json.gz                          | Bin
 .../WGS/F000002_2.ht/metadata.json.gz         | Bin 352 -> 352 bytes
 .../F000002_2.ht/rows/.metadata.json.gz.crc   | Bin 16 -> 16 bytes
 .../WGS/F000002_2.ht/rows/metadata.json.gz    | Bin 627 -> 630 bytes
 ...0-57b69294-ffdb-4b39-842a-adf898b62d31.crc | Bin 0 -> 12 bytes
 ...0-5efaaf66-a01a-4640-a3e4-aef656269368.crc | Bin 12 -> 0 bytes
 ...art-0-57b69294-ffdb-4b39-842a-adf898b62d31 | Bin 0 -> 206 bytes
 ...art-0-5efaaf66-a01a-4640-a3e4-aef656269368 | Bin 206 -> 0 bytes
 hail_search/queries/base.py                   |  52 +++++++-----
 hail_search/queries/mito.py                   |  80 ++++++++----------
 hail_search/test_utils.py                     |   2 +-
 18 files changed, 70 insertions(+), 79 deletions(-)
 rename hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/{part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx => part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx}/.index.crc (100%)
 rename hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/{part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx => part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx}/.metadata.json.gz.crc (100%)
 rename hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/{part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx => part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx}/index (100%)
 rename hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/{part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx => part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx}/metadata.json.gz (100%)
 create mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-57b69294-ffdb-4b39-842a-adf898b62d31.crc
 delete mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-5efaaf66-a01a-4640-a3e4-aef656269368.crc
 create mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-57b69294-ffdb-4b39-842a-adf898b62d31
 delete mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-5efaaf66-a01a-4640-a3e4-aef656269368

diff --git a/hail_search/definitions.py b/hail_search/definitions.py
index cfa3ee9cfa..7cc97d1a12 100644
--- a/hail_search/definitions.py
+++ b/hail_search/definitions.py
@@ -15,15 +15,8 @@ def family_entries_field(self) -> str:
     @property
     def failed_family_sample_field(self) -> str:
         return {
-            SampleType.WES: 'wes_failed_family_sample_indices',
-            SampleType.WGS: 'wgs_failed_family_sample_indices',
-        }[self]
-
-    @property
-    def passes_inheritance_field(self) -> str:
-        return {
-            SampleType.WES: 'wes_passes_inheritance',
-            SampleType.WGS: 'wgs_passes_inheritance',
+            SampleType.WES: 'wes_failed_family_sample_guids',
+            SampleType.WGS: 'wgs_failed_family_sample_guids',
         }[self]
 
     @property
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/.README.txt.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/.README.txt.crc
index f7799b94778f02019a04657be1cc91ebeb101949..b774b2827b5f9698c8ceb8bcb104c1f48138e580 100644
GIT binary patch
literal 12
TcmYc;N@ieSU}8v`{4o{)695B#

literal 12
TcmYc;N@ieSU}6yY%H|FL5ds2{

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/.metadata.json.gz.crc
index fee8fcb4687e14806f37b6d919092dba23677b46..5f2f901b97131b2aeb5048cac56077d681ae57cb 100644
GIT binary patch
literal 12
TcmYc;N@ieSU}6YqU<?HS5T^oV

literal 12
TcmYc;N@ieSU}E^xX(<H&6K?|v

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/README.txt b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/README.txt
index 3fea5d0da1..b8be820940 100644
--- a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/README.txt
+++ b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/README.txt
@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.130-bea04d9c79b5
-  Created at 2024/10/02 14:46:35
\ No newline at end of file
+  Written with version 0.2.132-678e1f52b999
+  Created at 2024/10/28 16:21:30
\ No newline at end of file
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/.index.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/.index.crc
similarity index 100%
rename from hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/.index.crc
rename to hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/.index.crc
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/.metadata.json.gz.crc
similarity index 100%
rename from hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/.metadata.json.gz.crc
rename to hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/.metadata.json.gz.crc
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/index b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/index
similarity index 100%
rename from hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/index
rename to hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/index
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/metadata.json.gz b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/metadata.json.gz
similarity index 100%
rename from hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-5efaaf66-a01a-4640-a3e4-aef656269368.idx/metadata.json.gz
rename to hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/index/part-0-57b69294-ffdb-4b39-842a-adf898b62d31.idx/metadata.json.gz
diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/metadata.json.gz b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/metadata.json.gz
index 8f5109cfbbaa719beb60c797355ad7c086d4b52e..c44e0dd8eeb67949e4b069250a02f03079077ae5 100644
GIT binary patch
delta 337
zcmV-X0j~bw0^kCW7=II-AH8#!nPt0hy6nafQsJm%wQbrmLrDMo4hTBE+6^i1dCt@J
zKt;B>faC{^&6Ol<I0}O?C3~KWOGqAjL9ZVM55v(I`rD^qGnq^XB?h)&K&D_510vDf
z?Ge7Dh&aAMy(=|f<+FaNc0z5qU@K>e)K!)rG!l7c+0+<bu75Gl<u0a$&bR~1R^ZNA
z3)eb!$~^sslC6bG3ro2WAi&1dsAK1ED(t;}-p!ZMJ{;e7+|7nK2!}Vm+7Kiz{*twF
z{=r_Q3j;cRW-mf<HyqH}qRr-?EJDAJy~pdP>Y$ZGizTcgr<*rR$q)5JmS3}|LslBn
zW~k>$cD%<_9ZLV-*TC4MxpBF}Pne{tXwT3J7F{W7Dz~zZUk~EiW0VHu;mU9h+n#GG
j%dN|0>O}blC1ix*?7(}pwf)V{(6str>M&i?g#rKoUI(f!

delta 337
zcmV-X0j~bw0^kCW7=KQjAH8#!nPt0hy6nafQp!=uDs9>_LrDMo4hTBE+6^i1dCt@J
zKt;Bhg!l)H%~Vd<XdDbCl<avXFCppo2EE6i|BwLh57Vg_Pm?D?iGeK`$OYKgfQ&VF
zdxS43B914hcclibeAX}3PO5}UwsxivuCn}~k;qcZX2$SxgMWFJ?;=|0lsm9&4ep$^
zaIIsf%+qfu*+wc+SjwdY2{xie9Xo$hVej?xZm|mY!Q{T<ZZ^b0IK1)IhLGdpFIg)W
zAM7=E!GO-5*^5-%jfQl-Y_r8D3(@Z*@A3LV9kj~PVhO9r>E_Kc=ZAVCtFL+3A!`ky
z8R~hG9q%z!$4dYAH83`5Zd~T@6UIUn?HO9ZvMYs6<yO}5n_*OYjM9KSTp7+`+jC8&
jnRQt%oGjm<gp@Fx9e9tnw!irqnpXb{WlT@{g#rKojq<A~

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/.metadata.json.gz.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/.metadata.json.gz.crc
index caf4248bc39fd6678d852baffee083d06b11a820..06d9e98f8ef007ecd9a867ce19d2f47714973285 100644
GIT binary patch
literal 16
XcmYc;N@ieSU}6Xtxo{z3&dN;yBiIF%

literal 16
XcmYc;N@ieSU}E_3?py2Xq+2ZjFBJy|

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/metadata.json.gz b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/metadata.json.gz
index c18fceb46be2b260ee2b9874e13c6452c7f4e278..75aaf792a6baad3fc0bef4dc8622e662d3fffcc8 100644
GIT binary patch
literal 630
zcmV-+0*U<}iwFP!000000NqwiZ`wc*{V#iJRg=axxVCSY5ELn@Qb0X4LTK@hVH;<S
z)=L$N{NFok<4>p*BIObe$bK_B^WN;Ub`M0*XCOYg6AWH}O@H3Zwh&sxAj>D%6aSIK
zNw`b#oyIZ5kdg(4!h}Jn6N!H)E6n#>V52I4S)d_|d>IEcg_)AOP#yAeehUf{q4-*3
zTu`|;wn@qrPXr=&LfKYk9D5@$l#=cr%hZJt@mPUO{gVI)B{@`qX1~b~zbI@B1AlxQ
zCsa9o<L046C-dV|w#c-OKSv!c1^4>@(_}i@*zV_wV9^W{xmefaW}qsp<W*%J8C8TD
zd@4F4tbZi4+C>q_&g}2UfoZux9WqF`;W2BZ1W5Y{8MKmC8l3UJnBWWswsX4dSE^XP
z^ul#04Cr%rWu|{9f@`;RG~AU~ZaxX|163Quudcr4=^BlJM!Cga<-6vdM_i_A$=OR`
zDx5FcyJe_47bE^VdNwnXC`v(9OsEivqQ}*Z9@%;S)lwQlT6WR`E;Vb#>V#8=%?B|c
zewc#B-_bX3GgRJBf;exX+_6ji{$bhK>{BBa$h(`aXd@v^Bs)*)LLXKWXnF5cc~^H=
z_2o`IC*?mvKB9SXXm31`@)^|AX;;aJF21Ew-Ew`<<JqrYde^<dx0T~rUcVPbY}M<p
zY_I3`E!v|jay@tDSj;x_d%^E16>A8RonU(Xfuss6Xko=I0v`$wW7lvaO{7zLnE2*(
z-}bWlqJjN~Bg_~Q+;Refy|RvH4ouT=opz}?=1lTRT!itCp}BKvs2wV7tea>g(`u+v
QQuoTTe|WRzO(zKe0M|P#UH||9

literal 627
zcmV-(0*w71iwFP!000000NqwiZ{jcz{VzW4YLk`_upl==DMG4NT|j%-3L!U{fVZiG
z9J4Bm^4~kocLJ44rC!PbC2z(v?~Pw%ABkYkKpZj?KD>ZG|9!LAf!8GlSwF#nI1eO@
zynT%CEDRxpn5;15MLu{skvPYq!t$^Ke_RGI3p9k09}}0wuuyXEsbgBsX+T~i6yIo!
z3nmZ7E{eJ0kw9c7l-*5?yf*?PDcRwnNL?8L4;9GRISGJJl0zA&_nZE5vcks5btboA
z#1!orH}?fPUFJ{8D$zRr<vJP)?)3k+>3qDk2j5GASu;%JVpEY@fGV+qSDBeJDhbv2
zlyt^eKPU6J4+4;_+22iEt2=P3kU_jH5B*w-i?pARK_lr=gA4v26KKD0)6->tV&$hx
zFI<PhfIYWYCi;gWxOQ7h!>qtk^GOKrnc5<Lb#<MlYcvEFq!xRZ@9KLVa2cyL_g^wo
z;e65F4MSDA7;!$)vxyM}K@6&7!i0zv%U9QWB<KBCNvR2G*hvex)T|||6HYBQU&Mg;
zVG0)hMBjYOP-#C2;=F}Y$FA}FhjnYSPmP!%pKiLWjRY@}{&`Xt`mmfp!+WR7+q&DT
zFL&xWDQ^h*isr?keegs|XHZS2StTL5_>M_+%k@EzXTN?iJ7ymO#sW%B*0Gq`qrHyF
zZ0MN`0@|ltI<)B^y%+qQGqC|T+6!N=KayBs1uZPQMc_l`VeIN{rG<0~4-?1g^z30$
zT{N)&Xp9*nf?G~N`0uPUwEC7s2eesgi8<4>5*J>$_tD%bHPj9zHqlKql4vzdDXDuU
N$tx--88asd000g{B9{OF

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-57b69294-ffdb-4b39-842a-adf898b62d31.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-57b69294-ffdb-4b39-842a-adf898b62d31.crc
new file mode 100644
index 0000000000000000000000000000000000000000..7b6b76d406cc2627893358ce61707360c0866abe
GIT binary patch
literal 12
TcmYc;N@ieSU}AVF>}&!65*Grl

literal 0
HcmV?d00001

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-5efaaf66-a01a-4640-a3e4-aef656269368.crc b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/.part-0-5efaaf66-a01a-4640-a3e4-aef656269368.crc
deleted file mode 100644
index d4dcde073f96bc3f5e9908e425b67b6ab38d26da..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12
TcmYc;N@ieSU}E^a_mM3C6{G|b

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-57b69294-ffdb-4b39-842a-adf898b62d31 b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-57b69294-ffdb-4b39-842a-adf898b62d31
new file mode 100644
index 0000000000000000000000000000000000000000..57088cd43339b536d15c8ceb6a6793a3753cf5ca
GIT binary patch
literal 206
zcmdnVz`*bWh&8tA|5f;r%F0l}!N|apoKa+WJdlaW(V5Yafti6pgu#Y|A(=sf=Yc(!
z$l+tVg_sya7~M4#pV%vWuvcmPctM+q(LGsz;og>SLbvRtc^HywukkKBk$%@+mF0uI
z22b1ei`tCRVS&LxAw`LK$r-7^egT%2dX}ao`Gy7tdIko}x-1M5EDTmPQi(g43m&tV
z<zWzDSiqCl@IWSm#X=~qo7t>^CxC4V^N}rFMyuz<bFf98XAtHEIvfPRj%Q$GU;qFd
C0Xhf(

literal 0
HcmV?d00001

diff --git a/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-5efaaf66-a01a-4640-a3e4-aef656269368 b/hail_search/fixtures/GRCh38/SNV_INDEL/families/WGS/F000002_2.ht/rows/parts/part-0-5efaaf66-a01a-4640-a3e4-aef656269368
deleted file mode 100644
index e113fa74e796762da26b63b59a9957b9f99af9dd..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 206
zcmdnVz`*bWh&8tA|5f;r%F0l}!N|apoKa+WJdlaW(V5Yafti6pgu#Y|A(=sf=Yc&J
z&*5Xcg_sya7~M4#pV%vWuvZaj{CGi|iP1e-f8pMiZ$h{1rFj^VYp?MxJCT0ZUX|s8
zy++&ii`tCRVS&LxAw`LK$r-7^egT%2dX}ao`Gy7tdIko}x-1M5EDTmPQi(g43m&tV
z<zWzDSiqCl@IWSmWshK7H?x_7Z~)sB<|A9Uj8@Ny=U|IG&mhbTbT|lr9nZkXzyJUk
CN;)zC

diff --git a/hail_search/queries/base.py b/hail_search/queries/base.py
index a85d5ba011..39836f3915 100644
--- a/hail_search/queries/base.py
+++ b/hail_search/queries/base.py
@@ -472,8 +472,8 @@ def _apply_entry_filters(ht):
     def _filter_single_entries_table(self, ht, project_families, inheritance_filter=None, quality_filter=None, is_merged_ht=False, **kwargs):
         ht, sorted_family_sample_data = self._add_entry_sample_families(ht, project_families, is_merged_ht)
         ht = self._filter_quality(ht, quality_filter, **kwargs)
-        ht, ch_ht, _, _ = self._filter_inheritance(
-            ht, None, inheritance_filter, sorted_family_sample_data,
+        ht, ch_ht = self._filter_inheritance(
+            ht, None, inheritance_filter, sorted_family_sample_data, self._annotate_families_inheritance
         )
         ht = self._apply_entry_filters(ht)
         ch_ht = self._apply_entry_filters(ch_ht)
@@ -573,7 +573,7 @@ def _get_sample_type(cls, family_index, ht_globals):
         return ht_globals.sample_type
 
     def _filter_inheritance(
-        self, ht, comp_het_ht, inheritance_filter, sorted_family_sample_data,
+        self, ht, comp_het_ht, inheritance_filter, sorted_family_sample_data, annotate_func,
         annotation='family_entries', entries_ht_field='family_entries'
     ):
         any_valid_entry = lambda x: self.GENOTYPE_QUERY_MAP[HAS_ALT](x.GT)
@@ -584,13 +584,12 @@ def _filter_inheritance(
             any_valid_entry = lambda x: prev_any_valid_entry(x) & (x.affected_id == AFFECTED_ID)
 
         ht = ht.annotate(**{
-            annotation: ht[entries_ht_field].map(
+            entries_ht_field: ht[entries_ht_field].map(
                 lambda entries: hl.or_missing(entries.any(any_valid_entry), entries)
             )})
 
-        ch_ht_entry_indices_by_gt = None
         if self._has_comp_het_search:
-            comp_het_ht, ch_ht_entry_indices_by_gt = self._annotate_families_inheritance(
+            comp_het_ht = annotate_func(
                 comp_het_ht if comp_het_ht is not None else ht, COMPOUND_HET, inheritance_filter,
                 sorted_family_sample_data, annotation, entries_ht_field
             )
@@ -599,17 +598,38 @@ def _filter_inheritance(
             # No sample-specific inheritance filtering needed
             sorted_family_sample_data = []
 
-        ht, ht_entry_indices_by_gt = (None, None) if self._inheritance_mode == COMPOUND_HET else self._annotate_families_inheritance(
+        ht = None if self._inheritance_mode == COMPOUND_HET else annotate_func(
             ht, self._inheritance_mode, inheritance_filter, sorted_family_sample_data,
             annotation, entries_ht_field
         )
 
-        return ht, comp_het_ht, ht_entry_indices_by_gt, ch_ht_entry_indices_by_gt
+        return ht, comp_het_ht
 
     def _annotate_families_inheritance(
         self, ht, inheritance_mode, inheritance_filter, sorted_family_sample_data,
         annotation, entries_ht_field,
     ):
+        entry_indices_by_gt = self._get_entry_indices_by_gt_map(
+            inheritance_filter, inheritance_mode, sorted_family_sample_data
+        )
+
+        for genotype, entry_indices in entry_indices_by_gt.items():
+            if not entry_indices:
+                continue
+            entry_indices = hl.dict(entry_indices)
+            ht = ht.annotate(**{
+                annotation: hl.enumerate(ht[entries_ht_field]).starmap(
+                    lambda family_i, family_samples: hl.or_missing(
+                        ~entry_indices.contains(family_i) | entry_indices[family_i].all(
+                            lambda sample_i: self.GENOTYPE_QUERY_MAP[genotype](family_samples[sample_i].GT)
+                        ), family_samples,
+                    ),
+                )
+            })
+
+        return ht
+
+    def _get_entry_indices_by_gt_map(self, inheritance_filter, inheritance_mode, sorted_family_sample_data):
         individual_genotype_filter = (inheritance_filter or {}).get('genotype')
 
         # Create a mapping of genotypes to check against a list of samples for a family
@@ -631,21 +651,7 @@ def _annotate_families_inheritance(
             ]
             self.max_unaffected_samples = max(family_unaffected_counts) if family_unaffected_counts else 0
 
-        for genotype, entry_indices in entry_indices_by_gt.items():
-            if not entry_indices:
-                continue
-            entry_indices = hl.dict(entry_indices)
-            ht = ht.annotate(**{
-                annotation: hl.enumerate(ht[entries_ht_field]).starmap(
-                    lambda family_i, family_samples: hl.or_missing(
-                        ~entry_indices.contains(family_i) | entry_indices[family_i].all(
-                            lambda sample_i: self.GENOTYPE_QUERY_MAP[genotype](family_samples[sample_i].GT)
-                        ), family_samples,
-                    ),
-                )
-            })
-
-        return ht, entry_indices_by_gt
+        return entry_indices_by_gt
 
     def _get_family_passes_quality_filter(self, quality_filter, ht, **kwargs):
         quality_filter = quality_filter or {}
diff --git a/hail_search/queries/mito.py b/hail_search/queries/mito.py
index 439e9dfce7..52af6212d4 100644
--- a/hail_search/queries/mito.py
+++ b/hail_search/queries/mito.py
@@ -206,41 +206,33 @@ def _filter_entries_ht_both_sample_types(
 
         ch_ht = None
         family_guid_idx_map = defaultdict(dict)
-        family_sample_idx_map = defaultdict(lambda: defaultdict(dict))
         for sample_type, sorted_family_sample_data in sample_types:
-            ht, ch_ht, ht_idx_by_gt_map, ch_idx_by_gt_map = self._filter_inheritance(
+            ht, ch_ht = self._filter_inheritance(
                 ht, ch_ht, inheritance_filter, sorted_family_sample_data,
-                annotation=sample_type.passes_inheritance_field, entries_ht_field=sample_type.family_entries_field
+                annotate_func=self._annotate_failed_family_samples_inheritance,
+                annotation=sample_type.failed_family_sample_field, entries_ht_field=sample_type.family_entries_field,
             )
-            ht = self._annotate_failed_family_samples_inheritance(
-                ht, ht_idx_by_gt_map,
-                annotation=sample_type.failed_family_sample_field, entries_ht_field=sample_type.family_entries_field
-            )
-            ch_ht = self._annotate_failed_family_samples_inheritance(
-                ch_ht, ch_idx_by_gt_map,
-                annotation=sample_type.failed_family_sample_field, entries_ht_field=sample_type.family_entries_field
-            )
-
             for family_idx, samples in enumerate(sorted_family_sample_data):
                 family_guid = samples[0]['familyGuid']
                 family_guid_idx_map[family_guid][sample_type.value] = family_idx
-                for sample_idx, sample in enumerate(samples):
-                    family_sample_idx_map[family_guid][sample['sampleId']][sample_type.value] = sample_idx
 
         family_guid_idx_map = hl.dict(family_guid_idx_map)
-        family_sample_idx_map = hl.dict(family_sample_idx_map)
-        ht = self._apply_multi_sample_type_entry_filters(ht, family_guid_idx_map, family_sample_idx_map)
-        ch_ht = self._apply_multi_sample_type_entry_filters(ch_ht, family_guid_idx_map, family_sample_idx_map)
+        ht = self._apply_multi_sample_type_entry_filters(ht, family_guid_idx_map)
+        ch_ht = self._apply_multi_sample_type_entry_filters(ch_ht, family_guid_idx_map)
         return ht, ch_ht
 
     def _annotate_failed_family_samples_inheritance(
-        self, ht, entry_indices_by_gt, annotation, entries_ht_field,
+        self, ht, inheritance_mode, inheritance_filter, sorted_family_sample_data, annotation, entries_ht_field
     ):
+        entry_indices_by_gt = self._get_entry_indices_by_gt_map(
+           inheritance_filter, inheritance_mode, sorted_family_sample_data
+        )
+
         if ht is None:
             return ht
 
         # Initialize empty array
-        ht = ht.annotate(**{annotation: ht[entries_ht_field].map(lambda x: hl.empty_array(hl.tint32))})
+        ht = ht.annotate(**{annotation: ht[entries_ht_field].map(lambda x: hl.empty_array(hl.tstr))})
 
         # Add failed genotype samples
         for genotype, entry_indices in entry_indices_by_gt.items():
@@ -252,23 +244,21 @@ def _annotate_failed_family_samples_inheritance(
                 lambda family_idx, entries: hl.bind(
                     lambda failed_samples: ht[annotation][family_idx].extend(failed_samples),
                     entry_indices.get(family_idx).filter(
-                        lambda sample_i: ~self.GENOTYPE_QUERY_MAP[genotype](entries[sample_i].GT)
-                    )
+                        lambda sample_idx: ~self.GENOTYPE_QUERY_MAP[genotype](entries[sample_idx].GT)
+                    ).map(lambda sample_idx: entries[sample_idx]['sampleId'])
                 )
             )})
 
         return ht
 
-    def _apply_multi_sample_type_entry_filters(self, ht, family_idx_map, sample_idx_map):
+    def _apply_multi_sample_type_entry_filters(self, ht, family_idx_map):
         if ht is None:
             return ht
 
         # Keep family from both sample types if either passes quality AND inheritance
         for sample_type in SampleType:
             ht = self._apply_quality_entry_filters(ht, sample_type, family_idx_map)
-            # TODO - Since each sample type is processed separately, wgs with 1 sample will not be filtered out if it passes in wes (even though another sample failed in wes)
-            # and the coalesce below keeps that sample even though the family was filtered out in wes. This is a limitation of the current implementation.
-            ht = self._apply_inheritance_entry_filters(ht, sample_type, family_idx_map, sample_idx_map)
+            ht = self._apply_inheritance_entry_filters(ht, sample_type, family_idx_map)
 
         # Merge family entries and filters from both sample types
         ht = ht.transmute(
@@ -302,28 +292,30 @@ def _family_has_valid_quality(ht, sample_type, sample_type_family_idx):
             hl.is_defined(ht[sample_type.passes_quality_field][sample_type_family_idx])
         )
 
-    def _apply_inheritance_entry_filters(self, ht, sample_type, family_idx_map, sample_idx_map):
+    @staticmethod
+    def _apply_inheritance_entry_filters(ht, sample_type, family_idx_map):
         ht = ht.annotate(
             **{sample_type.family_entries_field: hl.enumerate(ht[sample_type.family_entries_field]).starmap(
-                lambda family_idx, family_samples: hl.or_missing( # Keep a family if
-                    hl.all(hl.enumerate(family_samples).starmap(  # For each sample in the family,
-                        lambda sample_idx, sample: hl.bind(lambda other_sample_type_indices: ( # Get the sample and family index of the sample in the other sample type family_entries
-                            hl.if_else(
-                                hl.is_defined(sample_idx) & hl.is_defined(other_sample_type_indices[1]), # If samples are present for both sample types,
-                                (  # Keep the family entries if family passes inheritance in either sample type.
-                                    hl.is_defined(ht[sample_type.passes_inheritance_field][family_idx]) |
-                                    hl.is_defined(ht[sample_type.other_sample_type.passes_inheritance_field][other_sample_type_indices[0]])
-                                ),  # Else, if sample is in only one sample type, check if that sample did not fail inheritance in either sample type
-                                self._family_sample_has_valid_inheritance(ht, sample_type, family_idx, sample_idx) |
-                                self._family_sample_has_valid_inheritance(ht, sample_type.other_sample_type, other_sample_type_indices[0], other_sample_type_indices[1])
-                            )
-                        ),(
-                            family_idx_map.get(hl.coalesce(sample)['familyGuid']).get(sample_type.other_sample_type.value),
-                            sample_idx_map.get(hl.coalesce(sample)['familyGuid']).get(hl.coalesce(sample)['sampleId']).get(sample_type.other_sample_type.value)),
+                lambda family_idx, family_samples: hl.or_missing(
+                    hl.bind(lambda other_sample_type_family_idx: (
+                        hl.bind(
+                            lambda other_sample_type_pass_samples, sample_type_pass_samples: (
+                                ht[sample_type.failed_family_sample_field][family_idx].all(
+                                    other_sample_type_pass_samples.contains
+                                ) & ht[sample_type.other_sample_type.failed_family_sample_field][other_sample_type_family_idx].all(
+                                    sample_type_pass_samples.contains
+                                )),
+                            ht[sample_type.other_sample_type.family_entries_field][other_sample_type_family_idx].filter(
+                                lambda s: ~ht[sample_type.other_sample_type.failed_family_sample_field][other_sample_type_family_idx].contains(s['sampleId'])
+                            ).map(lambda s: s['sampleId']),
+                            ht[sample_type.other_sample_type.family_entries_field][family_idx].filter(
+                                lambda s: ~ht[sample_type.failed_family_sample_field][family_idx].contains(s['sampleId'])
+                            ).map(lambda s: s['sampleId']),
                         )
-                )), family_samples)
-            )
-        })
+                    ), family_idx_map.get(hl.coalesce(family_samples)[0]['familyGuid']).get(sample_type.other_sample_type.value)
+                ), family_samples)
+            )}
+        )
         return ht
 
     @staticmethod
diff --git a/hail_search/test_utils.py b/hail_search/test_utils.py
index 6895b8df25..7116ca8308 100644
--- a/hail_search/test_utils.py
+++ b/hail_search/test_utils.py
@@ -165,7 +165,7 @@
 VARIANT1_BOTH_SAMPLE_TYPES['genotypes'] = {
     'I000004_hg00731': [
         genotypes['I000004_hg00731'],
-        {**genotypes['I000004_hg00731'], 'sampleType': 'WGS'}
+        {**genotypes['I000004_hg00731'], 'numAlt': 2, 'sampleType': 'WGS'}
     ],
     'I000005_hg00732': [
         genotypes['I000005_hg00732'],