close #123

brentp · Sep 20, 2023 · 7740a33 · 7740a33
1 parent de50b1c
commit 7740a33
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git 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
@@ -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
@@ -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
@@ -1 +1 @@
-let somalierVersion* = "0.2.18"
+let somalierVersion* = "0.2.19"