From 7740a33a2a0ae35302d223e9dbf14f7e2c353cd5 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Wed, 20 Sep 2023 11:01:23 +0200
Subject: [PATCH] close #123

---
 CHANGES.md                  | 4 ++++
 somalier.nimble             | 2 +-
 src/somalierpkg/relate.nim  | 6 +++++-
 src/somalierpkg/version.nim | 2 +-
 4 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index aac24ad..23ebfba 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,7 @@
+v0.2.19
+=======
++ [relate/infer] fix check that would prevent some inference (#123)
+
 v0.2.18
 =======
 + [find_sites] handle empty alternate alleles (#121)
diff --git a/somalier.nimble b/somalier.nimble
index 522bc31..03bd6d5 100644
--- a/somalier.nimble
+++ b/somalier.nimble
@@ -1,6 +1,6 @@
 #import somalierpkg/version as _
 
-version       = "0.2.18" #somalierVersion
+version       = "0.2.19" #somalierVersion
 author        = "Brent Pedersen"
 description   = "sample-swap checking directly on BAMs/CRAMs for cancer data"
 license       = "MIT"
diff --git a/src/somalierpkg/relate.nim b/src/somalierpkg/relate.nim
index ff42e84..4be879b 100644
--- a/src/somalierpkg/relate.nim
+++ b/src/somalierpkg/relate.nim
@@ -456,7 +456,10 @@ proc high_quality(gt_counts: array[5, seq[uint16]], i:int): bool {.inline.} =
   result = gt_counts[4][i].float / (gt_counts[0][i] + gt_counts[1][i] + gt_counts[2][i] + gt_counts[3][i] + gt_counts[4][i]).float < 0.06
   if not result:
     return false
-  result = gt_counts[2][i].float / gt_counts[1][i].float > 0.7
+
+  # should have fewer hom-alts[2] than hets[1]
+  result = gt_counts[2][i].float / gt_counts[1][i].float < 0.7
+
 
 proc samples_have_y_depth(stats: seq[Stat4]): bool =
   var n = 0
@@ -821,6 +824,7 @@ proc write_ped(fh:File, final: var relation_matrices, stats: seq[Stat4], gt_coun
   fh.write("X_depth_mean\tX_n\tX_hom_ref\tX_het\tX_hom_alt\t")
   fh.write("Y_depth_mean\tY_n\n")
 
+
   if infer:
     final.remove_spurious_parent_ids(L, stats)
     for i, sample_name in L.sample_names:
diff --git a/src/somalierpkg/version.nim b/src/somalierpkg/version.nim
index 3cf73c1..b14b446 100644
--- a/src/somalierpkg/version.nim
+++ b/src/somalierpkg/version.nim
@@ -1 +1 @@
-let somalierVersion* = "0.2.18"
+let somalierVersion* = "0.2.19"