diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml index 0711080d..4be2ac36 100644 --- a/.github/workflows/format.yml +++ b/.github/workflows/format.yml @@ -10,7 +10,7 @@ jobs: - name: Setup Java uses: actions/setup-java@v4 with: - java-version: '11' + java-version: '21' distribution: 'temurin' architecture: x64 - name: Cache m2 repository diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ef408006..fa135f3c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: [ '8', '11', '17', '20'] + java: [ '8', '11', '17', '21'] name: Java ${{ matrix.java }} steps: - uses: actions/checkout@v4 diff --git a/project.clj b/project.clj index e5761eb5..3d25240e 100644 --- a/project.clj +++ b/project.clj @@ -3,25 +3,25 @@ :url "https://github.com/chrovis/cljam" :license {:name "Apache License, Version 2.0" :url "https://www.apache.org/licenses/LICENSE-2.0"} - :dependencies [[org.clojure/core.memoize "1.0.257"] - [org.clojure/tools.logging "1.2.4"] - [org.clojure/tools.cli "1.0.214"] - [org.apache.commons/commons-compress "1.23.0"] + :dependencies [[org.clojure/core.memoize "1.1.266"] + [org.clojure/tools.logging "1.3.0"] + [org.clojure/tools.cli "1.1.230"] + [org.apache.commons/commons-compress "1.26.1"] [clj-sub-command "0.6.0"] [digest "1.4.10"] [bgzf4j "0.1.2"] [com.climate/claypoole "1.1.4"] [camel-snake-kebab "0.4.3"] - [proton "0.2.2"]] - :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.1"] + [proton "0.2.3"]] + :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.3"] [cavia "0.5.1"] [criterium "0.4.6"] [net.totakke/libra "0.1.1"] [se.haleby/stub-http "0.2.14"]] - :plugins [[lein-binplus "0.6.6" :exclusions [org.clojure/clojure]] - [lein-codox "0.10.7"] - [lein-marginalia "0.9.1" :exclusions [org.clojure/clojure]] - [lein-cloverage "1.1.2"] + :plugins [[lein-binplus "0.6.8" :exclusions [org.clojure/clojure]] + [lein-codox "0.10.8"] + [lein-marginalia "0.9.2" :exclusions [org.clojure/clojure]] + [lein-cloverage "1.2.4"] [net.totakke/lein-libra "0.1.2"] [lein-cljfmt "0.9.2"]] :test-selectors {:default #(not-any? % [:slow :remote]) @@ -35,9 +35,9 @@ :1.8 {:dependencies [[org.clojure/clojure "1.8.0"]]} :1.9 {:dependencies [[org.clojure/clojure "1.9.0"]]} :1.10 {:dependencies [[org.clojure/clojure "1.10.3"]]} - :uberjar {:dependencies [[org.clojure/clojure "1.11.1"] - [org.apache.logging.log4j/log4j-api "2.20.0"] - [org.apache.logging.log4j/log4j-core "2.20.0"]] + :uberjar {:dependencies [[org.clojure/clojure "1.11.3"] + [org.apache.logging.log4j/log4j-api "2.23.1"] + [org.apache.logging.log4j/log4j-core "2.23.1"]] :resource-paths ["bin-resources"] :main cljam.tools.main :jvm-opts ["-Dclojure.compiler.direct-linking=true"] diff --git a/src/cljam/io/wig.clj b/src/cljam/io/wig.clj index 272282aa..09ee1687 100644 --- a/src/cljam/io/wig.clj +++ b/src/cljam/io/wig.clj @@ -89,12 +89,12 @@ (let [type' (->> fields rest fields->map :type)] (if (= type' "wiggle_0") (deserialize (rest lines) pre-start {:line line}) - (throw "The track type with version must be `wiggle_0`"))) + (throw (ex-info "The track type with version must be `wiggle_0`" {})))) ; declaration line of variableStep "variableStep" (let [{:keys [chrom span] - :or {span 1}} (->> fields rest fields->map) + :or {span "1"}} (->> fields rest fields->map) span (as-long span) track (assoc track :format :variable-step :chr chrom @@ -105,7 +105,7 @@ ; declaration line of fixedStep "fixedStep" (let [{:keys [chrom start span step] - :or {span 1, step 1}} (->> fields rest fields->map) + :or {span "1", step "1"}} (->> fields rest fields->map) step (long (as-long step)) pre-start (- (long (as-long start)) step) span (as-long span)