From 4a59997308433345caea2722d5e48b4fd8ecb7e3 Mon Sep 17 00:00:00 2001
From: Eric Weitz <eric.m.weitz@gmail.com>
Date: Thu, 10 Sep 2020 22:47:04 -0400
Subject: [PATCH] Use centromere position ratio, not raw position, to account
 for small genomes like yeast

---
 src/js/views/chromosome-model.js | 41 ++++++++++++++++----------------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/src/js/views/chromosome-model.js b/src/js/views/chromosome-model.js
index fb3fab08..dd42670f 100644
--- a/src/js/views/chromosome-model.js
+++ b/src/js/views/chromosome-model.js
@@ -130,32 +130,33 @@ function deleteExtraneousBands(chr, hasBands) {
 
 function getCentromerePosition(hasBands, bands) {
 
-  const hasTelocentricPArm = (
-    // As with almost all mouse chromosome, chimpanzee chr22
-    hasBands && bands[0].name[0] === 'p' && bands[1].name[0] === 'q' &&
-    bands[0].bp.stop - bands[0].bp.start < 2E6
-  );
-
-  let hasTelocentricQArm = false;
-  if (hasBands) {
-    // As with Macaca mulatta chromosome Y
-    const lastBand = bands.slice(-1)[0];
-    const penultimateBand = bands.slice(-2)[0];
+  if (hasBands === false) return '';
 
-    hasTelocentricQArm = (
-      hasBands && penultimateBand.name[0] === 'p' && lastBand.name[0] === 'q' &&
-      lastBand.bp.stop - lastBand.bp.start < 2E6
-    );
-  }
+  // As with Macaca mulatta chromosome Y
+  const firstBand = bands[0];
+  const lastBand = bands.slice(-1)[0];
+  const chrLength = lastBand.bp.stop - firstBand.bp.start;
+  const smallLength = chrLength/10;
 
-  if (hasTelocentricPArm) {
+  if (
     // As with almost all mouse chromosome, chimpanzee chr22
+    firstBand.name[0] === 'p' && bands[1].name[0] === 'q' &&
+    firstBand.bp.stop - firstBand.bp.start < smallLength
+  ) {
     return 'telocentric-p';
-  } else if (hasTelocentricQArm) {
+  }
+
+  const penultimateBand = bands.slice(-2)[0];
+
+  if (
+    penultimateBand.name[0] === 'p' && lastBand.name[0] === 'q' &&
+    lastBand.bp.stop - lastBand.bp.start < smallLength
+  ) {
+    // As with Macaca mulatta chromosome Y
     return 'telocentric-q';
-  } else {
-    return '';
   }
+
+  return '';
 }
 
 /**