Merge pull request #111 from GMOD/fix_off_by_one

Fix off-by-one in CRAM range request
GMOD · May 16, 2022 · dafd115 · dafd115
2 parents 8e61079 + 22ba4ea
commit dafd115
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Showing 4 changed files with 13 additions and 1 deletion.
diff --git a/src/craiIndex.js b/src/craiIndex.js
@@ -161,7 +161,7 @@ export default class CraiIndex {
     const compare = entry => {
       const entryStart = entry.start
       const entryEnd = entry.start + entry.span
-      if (entryStart >= queryEnd) {
+      if (entryStart > queryEnd) {
         return -1
       } // entry is ahead of query
       if (entryEnd <= queryStart) {

diff --git a/test/data/volvox-long-reads-sv.cram b/test/data/volvox-long-reads-sv.cram
diff --git a/test/data/volvox-long-reads-sv.cram.crai b/test/data/volvox-long-reads-sv.cram.crai
diff --git a/test/indexedfile.test.ts b/test/indexedfile.test.ts
@@ -440,3 +440,15 @@ describe('cram31', () => {
     expect(feature).toMatchSnapshot()
   })
 })
+
+test('start of chr', async () => {
+  const cram = new IndexedCramFile({
+    cramFilehandle: testDataFile('volvox-long-reads-sv.cram'),
+    index: new CraiIndex({
+      filehandle: testDataFile('volvox-long-reads-sv.cram.crai'),
+    }),
+  })
+
+  const feats = await cram.getRecordsForRange(0, 0, 1)
+  expect(feats.length).toBe(13)
+})