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Fix/improve find chain block #139

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Merged
nokara26 merged 2 commits into from
Dec 9, 2025
Merged

Fix/improve find chain block #139

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42e77ff
test: Add vcf-lift bench.
niyarin Dec 3, 2025
ecfc682
fix: Imrpove performance of finding a block in the indexed chain.
niyarin Nov 20, 2025
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21 changes: 21 additions & 0 deletions bench/varity/large_vcf_lift_bench.clj
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@@ -0,0 +1,21 @@
(ns varity.large-vcf-lift-bench
(:require [libra.bench :refer [defbench is]]
[libra.criterium :as c]
[cljam.io.sequence :as cseq]
[cljam.io.vcf :as vcf]
[varity.chain :as ch]
[varity.vcf-lift :as vcf-lift]
[varity.t-common
:refer [test-ref-seq-file
test-large-vcf-file
test-large-chain-file
prepare-cavia!]]))

(defbench large-vcf-lift-bench
(prepare-cavia!)
(with-open [seq-rdr (cseq/reader test-ref-seq-file)
vcf-rdr (vcf/reader test-large-vcf-file)]
(let [chidx (ch/index (ch/load-chain test-large-chain-file))]
(is (c/quick-bench
(doall (vcf-lift/liftover-variants
seq-rdr chidx (vcf/read-variants vcf-rdr))))))))
29 changes: 14 additions & 15 deletions src/varity/chain.clj
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Expand Up @@ -5,9 +5,9 @@
(:require [clojure.java.io :as io]
[clojure.string :as string]
[cljam.util.chromosome :refer [normalize-chromosome-key]]
[cljam.util.intervals :as intervals]
[proton.core :refer [as-long]]
[varity.util :as util])
(:import [clojure.lang Sorted]))
[varity.util :as util]))

(defn- update-multi
[m ks f]
Expand Down Expand Up @@ -81,7 +81,9 @@
(recur (->> (assoc d :t-start curr-t-start
:q-start curr-q-start
:t-end (+ curr-t-start (:size d))
:q-end (+ curr-q-start (:size d)))
:q-end (+ curr-q-start (:size d))
:start curr-t-start
:end (+ curr-t-start (:size d)))
(conj! results))
(first r)
(next r)
Expand All @@ -93,11 +95,11 @@
(:q-end header))))))

(defn- index-chain [chain]
(->> chain
cumsum-chain
(map (juxt :t-start identity))
(into (sorted-map))
(assoc chain :data)))
(assoc chain
:data
(-> chain
cumsum-chain
(intervals/index-intervals {:structure :nclist}))))

(defn index
"Creates chain index for search."
Expand All @@ -109,12 +111,11 @@
(mapv index-chain xs)])))))

;;; Search

(defn- in-block?
[pos {:keys [^Sorted data header] :as chain}]
[pos {:keys [data header] :as chain}]
(when (<= (inc (:t-start header)) pos (:t-end header))
(when-let [[start m] (first (. data seqFrom pos false))]
(when (<= start pos (dec (+ start (:size m))))
(when-let [m (first (intervals/find-overlap-intervals data nil pos (inc pos)))]
(when (<= (:t-start m) pos (dec (+ (:t-start m) (:size m))))
(assoc chain :in-block m)))))

(def ^:private normalize-chr (memoize normalize-chromosome-key))
Expand All @@ -137,6 +138,4 @@
(defn search-overlap-blocks
"Calculates a list of blocks that overlap the given interval."
[start end blocks-idx]
(->> (subseq blocks-idx <= end)
(map second)
(filter #(> (:t-end %) start))))
(intervals/find-overlap-intervals blocks-idx nil (inc start) end))
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40 changes: 21 additions & 19 deletions test/varity/chain_test.clj
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@@ -1,14 +1,18 @@
(ns varity.chain-test
(:require [clojure.test :refer :all]
[cljam.util.intervals :as intervals]
[varity.chain :as chain]))

(def ^:private sample-indexed-block
(sorted-map
2 {:t-start 2 :t-end 5}
6 {:t-start 6 :t-end 10}
8 {:t-start 8 :t-end 12}
14 {:t-start 14 :t-end 16}
18 {:t-start 18 :t-end 20}))
(intervals/index-intervals
(map (fn [{:keys [t-start t-end] :as m}]
(assoc m :start t-start :end t-end))
[{:t-start 2 :t-end 5}
{:t-start 6 :t-end 10}
{:t-start 8 :t-end 12}
{:t-start 14 :t-end 16}
{:t-start 18 :t-end 20}])
{:structure :nclist}))

(def ^:private ^:const sample-indexed-chain
{"chr1" [{:header {:t-name "chr1", :t-start 0, :t-end 100 :score 1}}
Expand All @@ -19,19 +23,17 @@
"chr3" [{:header {:t-name "chr2", :t-start 0, :t-end 300 :score 1}}]})

(deftest search-overlap-blocks-test
(is (= (chain/search-overlap-blocks 7 12 sample-indexed-block)
[{:t-start 6, :t-end 10} {:t-start 8, :t-end 12}]))
(is (= (chain/search-overlap-blocks 15 17 sample-indexed-block)
[{:t-start 14, :t-end 16}]))
(is (= (chain/search-overlap-blocks 6 7 sample-indexed-block)
[{:t-start 6, :t-end 10}]))
(is (= (chain/search-overlap-blocks 4 4 sample-indexed-block)
[{:t-start 2, :t-end 5}]))
(is (= (chain/search-overlap-blocks 5 5 sample-indexed-block) []))
(is (= (chain/search-overlap-blocks 6 6 sample-indexed-block)
[{:t-start 6, :t-end 10}]))
(is (= (chain/search-overlap-blocks 1 1 sample-indexed-block) []))
(is (= (chain/search-overlap-blocks 30 31 sample-indexed-block) [])))
(are [start end ans] (= (map #(select-keys % [:t-start :t-end])
(chain/search-overlap-blocks start end sample-indexed-block))
ans)
7 12 [{:t-start 6, :t-end 10} {:t-start 8, :t-end 12}]
15 17 [{:t-start 14, :t-end 16}]
6 7 [{:t-start 6, :t-end 10}]
4 4 [{:t-start 2, :t-end 5}]
5 5 []
6 6 [{:t-start 6, :t-end 10}]
1 1 []
30 31 []))

(deftest search-containing-chains-test
(is (= (chain/search-containing-chains "chr1" 10 20 sample-indexed-chain)
Expand Down
4 changes: 4 additions & 0 deletions test/varity/t_common.clj
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Expand Up @@ -73,3 +73,7 @@
(def test-load-refgene-file "./test-resources/test-refgene.txt")

(def test-load-refseq-file "./test-resources/test-refseq.txt")

(def test-large-chain-file "./test-resources/large.chain.gz")

(def test-large-vcf-file "./test-resources/large.vcf.gz")
4 changes: 2 additions & 2 deletions test/varity/vcf_lift_test.clj
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Expand Up @@ -10,14 +10,14 @@
[{:header {:t-name "chr1", :t-start 0, :t-end 540, :t-size 540,
:q-name "chr1", :q-start 0, :q-end 540, :q-size 540,
:q-strand :reverse}
:data [{:chr "chr1", :size 540, :dt nil, :dq nil}]}]))
:data [{:size 540, :dt nil, :dq nil}]}]))

(def small-forward-chains
(ch/index
[{:header {:t-name "chr1", :t-start 0, :t-end 540, :t-size 540,
:q-name "chr1", :q-start 0, :q-end 540, :q-size 540,
:q-strand :forward}
:data [{:chr "chr1", :size 540, :dt nil, :dq nil}]}]))
:data [{:size 540, :dt nil, :dq nil}]}]))

(deftest small-new-interval-test
(testing "reverse"
Expand Down