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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| (ns cljam.algo.cram-indexer-test | ||
| (:require [cljam.algo.cram-indexer :as indexer] | ||
| [cljam.io.crai :as crai] | ||
| [cljam.io.cram :as cram] | ||
| [cljam.test-common :as common] | ||
| [cljam.util :as util] | ||
| [clojure.java.io :as io] | ||
| [clojure.test :refer [deftest is]])) | ||
|
|
||
| (defn- read-index-entries [f] | ||
| (with-open [r (io/reader (util/compressor-input-stream f))] | ||
| (doall (#'crai/read-index-entries r)))) | ||
|
|
||
| (deftest create-index-test | ||
| (let [f (io/file common/temp-dir "medium.cram.crai")] | ||
| (common/with-before-after {:before (common/prepare-cache!) | ||
| :after (common/clean-cache!)} | ||
| (is (thrown-with-msg? Exception #"Cannot create CRAM index file .*" | ||
| (indexer/create-index common/medium-cram-file f))) | ||
| (indexer/create-index common/medium-cram-file f | ||
| :skip-sort-order-check? true) | ||
| (is (= (read-index-entries common/medium-crai-file) | ||
| (read-index-entries f)))))) | ||
|
|
||
| (deftest cram-without-alignments-test | ||
| (common/with-before-after {:before (common/prepare-cache!) | ||
| :after (common/clean-cache!)} | ||
| (let [header {:HD {:SO "coordinate"} | ||
| :SQ [{:SN "chr1", :LN 100}]} | ||
| target (io/file common/temp-dir "no_aln.cram") | ||
| target-crai (io/file common/temp-dir "no_aln.cram.crai")] | ||
| (with-open [w (cram/writer target)] | ||
| (cram/write-header w header) | ||
| (cram/write-refs w header)) | ||
| (is (common/not-throw? (indexer/create-index target target-crai)))))) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| (ns cljam.io.cram.writer-test | ||
| (:require [cljam.io.cram.encode.record :as record] | ||
| [cljam.io.cram.writer :as writer] | ||
| [clojure.test :refer [deftest is testing]])) | ||
|
|
||
| (deftest container-index-entries-test | ||
| (testing "no multiple reference slices" | ||
| (is (= [{:ref-seq-id 0, :start 123, :span 456 | ||
| :container-offset 100, :slice-offset 200, :size 1000} | ||
| {:ref-seq-id 0, :start 987, :span 654 | ||
| :container-offset 100, :slice-offset 1200, :size 900} | ||
| {:ref-seq-id 1, :start 1234, :span 5678 | ||
| :container-offset 100, :slice-offset 2100, :size 1100}] | ||
| (#'writer/container-index-entries | ||
| 100 | ||
| {:landmarks [200 1200 2100]} | ||
| [{:header {:ref-seq-id 0, :start 123, :span 456} | ||
| :size 1000} | ||
| {:header {:ref-seq-id 0, :start 987, :span 654} | ||
| :size 900} | ||
| {:header {:ref-seq-id 1, :start 1234, :span 5678} | ||
| :size 1100}] | ||
| [[{::record/ref-index 0, :pos 123 ::record/end 273} | ||
| {::record/ref-index 0, :pos 428 ::record/end 578}] | ||
| [{::record/ref-index 0, :pos 987 ::record/end 1137} | ||
| {::record/ref-index 0, :pos 1490 ::record/end 1640}] | ||
| [{::record/ref-index 1, :pos 1234 ::record/end 1384} | ||
| {::record/ref-index 1, :pos 6761 ::record/end 6911}]]))) | ||
| (is (= [{:ref-seq-id -1, :start 0, :span 0 | ||
| :container-offset 100, :slice-offset 200, :size 1000} | ||
| {:ref-seq-id -1, :start 0, :span 0 | ||
| :container-offset 100, :slice-offset 1200, :size 900}] | ||
| (#'writer/container-index-entries | ||
| 100 | ||
| {:landmarks [200 1200]} | ||
| [{:header {:ref-seq-id -1, :start 0, :span 0} | ||
| :size 1000} | ||
| {:header {:ref-seq-id -1, :start 0, :span 0} | ||
| :size 900}] | ||
| [[{::record/ref-index -1, :pos 0 ::record/end 0} | ||
| {::record/ref-index -1, :pos 0 ::record/end 0}] | ||
| [{::record/ref-index -1, :pos 0 ::record/end 0} | ||
| {::record/ref-index -1, :pos 0 ::record/end 0}]])))) | ||
| (testing "some multiple reference slices" | ||
| (is (= [{:ref-seq-id 0, :start 123, :span 456 | ||
| :container-offset 100, :slice-offset 200, :size 1000} | ||
| {:ref-seq-id 0, :start 987, :span 654 | ||
| :container-offset 100, :slice-offset 1200, :size 900} | ||
| {:ref-seq-id 1, :start 1234, :span 5678 | ||
| :container-offset 100, :slice-offset 1200, :size 900} | ||
| ;; Both of :start/:span should be zero for unmapped slices in respect of | ||
| ;; the CRAM specification, but it's guaranteed by the CRAI writer, | ||
| ;; so it doesn't matter what values these keys actually take here | ||
| {:ref-seq-id -1, :start 0, :span 1 | ||
| :container-offset 100, :slice-offset 1200, :size 900}] | ||
| (#'writer/container-index-entries | ||
| 100 | ||
| {:landmarks [200 1200]} | ||
| [{:header {:ref-seq-id 0, :start 123, :span 456} | ||
| :size 1000} | ||
| {:header {:ref-seq-id -2, :start 0, :span 0} | ||
| :size 900}] | ||
| [[{::record/ref-index 0, :pos 123 ::record/end 273} | ||
| {::record/ref-index 0, :pos 428 ::record/end 578}] | ||
| [{::record/ref-index 0, :pos 987 ::record/end 1138} | ||
| {::record/ref-index 0, :pos 1490 ::record/end 1640} | ||
| {::record/ref-index 1, :pos 1234 ::record/end 1384} | ||
| {::record/ref-index 1, :pos 6761 ::record/end 6911} | ||
| {::record/ref-index -1, :pos 0 ::record/end 0} | ||
| {::record/ref-index -1, :pos 0 ::record/end 0}]]))))) |
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