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Rename test namespaces to conventional names #105

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Sep 4, 2017
Merged

Rename test namespaces to conventional names #105

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4 changes: 2 additions & 2 deletions test/cljam/algo/t_bam_indexer.clj → test/cljam/algo/bam_indexer_test.clj
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(ns cljam.algo.t-bam-indexer
(ns cljam.algo.bam-indexer-test
"Tests for cljam.algo.bam-indexer."
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.sam :as sam]
[cljam.algo.sorter :as sorter]
[cljam.algo.bam-indexer :as bai]))
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_dedupe.clj → test/cljam/algo/dedupe_test.clj
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(ns cljam.algo.t-dedupe
(ns cljam.algo.dedupe-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.algo.dedupe :as dedupe]))

(deftest simple-pe-dedupe
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_depth.clj → test/cljam/algo/depth_test.clj
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(ns cljam.algo.t-depth
(ns cljam.algo.depth-test
(:require [clojure.test :refer :all]
[cljam.t-common :as common]
[cljam.test-common :as common]
[cljam.io.sam :as sam]
[cljam.algo.depth :as depth])
(:import [clojure.lang LazySeq ArraySeq]))
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_dict.clj → test/cljam/algo/dict_test.clj
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(ns cljam.algo.t-dict
(ns cljam.algo.dict-test
"Tests for cljam.algo.dict."
(:require [clojure.test :refer :all]
[clojure.string :as string]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.algo.dict :as dict]))

(defn same-dict-file? [f1 f2]
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_fasta_indexer.clj → test/cljam/algo/fasta_indexer_test.clj
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(ns cljam.algo.t-fasta-indexer
(ns cljam.algo.fasta-indexer-test
"Tests for cljam.fasta-indexer."
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.algo.fasta-indexer :as fai]))

(def temp-fa-file (str temp-dir "/test.fa"))
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_normal.clj → test/cljam/algo/normal_test.clj
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(ns cljam.algo.t-normal
(ns cljam.algo.normal-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.algo.normal :refer :all]
[cljam.io.sam :as sam]))

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4 changes: 2 additions & 2 deletions test/cljam/algo/t_pileup.clj → test/cljam/algo/pileup_test.clj
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(ns cljam.algo.t-pileup
(ns cljam.algo.pileup-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.sam :as sam]
[cljam.io.sequence :as cseq]
[cljam.algo.pileup :as plp]
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4 changes: 2 additions & 2 deletions test/cljam/algo/t_sorter.clj → test/cljam/algo/sorter_test.clj
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(ns cljam.algo.t-sorter
(ns cljam.algo.sorter-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.sam :as sam]
[cljam.algo.sorter :as sorter])
(:import [java.io Closeable]))
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4 changes: 2 additions & 2 deletions test/cljam/io/t_bam_index.clj → test/cljam/io/bam_index_test.clj
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(ns cljam.io.t-bam-index
(ns cljam.io.bam-index-test
"Tests for cljam.io.bam-index."
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.bam-index :as bai]))

;;; bin-index
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2 changes: 1 addition & 1 deletion test/cljam/io/bcf/t_writer.clj → test/cljam/io/bcf/writer_test.clj
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(ns cljam.io.bcf.t-writer
(ns cljam.io.bcf.writer-test
(:require [clojure.test :refer :all]
[cljam.io.bcf.writer :as bcf-writer])
(:import [java.nio ByteBuffer]))
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4 changes: 2 additions & 2 deletions test/cljam/io/t_bed.clj → test/cljam/io/bed_test.clj
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(ns cljam.io.t-bed
(ns cljam.io.bed-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.bed :as bed]
[cljam.io.sam :as sam]
[cljam.io.sam.util :as sam-util]
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4 changes: 2 additions & 2 deletions test/cljam/io/fasta/t_core.clj → test/cljam/io/fasta/core_test.clj
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(ns cljam.io.fasta.t-core
(ns cljam.io.fasta.core-test
(:require [clojure.test :refer :all]
[clojure.string :as cstr]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.fasta.core :as fa-core]))

(def illegal-fasta-file test-tabix-file)
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4 changes: 2 additions & 2 deletions test/cljam/io/t_fastq.clj → test/cljam/io/fastq_test.clj
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(ns cljam.io.t-fastq
(ns cljam.io.fastq-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[clojure.java.io :as cio]
[cljam.io.fastq :as fq]))

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4 changes: 2 additions & 2 deletions test/cljam/io/sam/t_util.clj → test/cljam/io/sam/util_test.clj
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(ns cljam.io.sam.t-util
(ns cljam.io.sam.util-test
"Tests for cljam.io.sam.util."
(:require [clojure.test :refer :all]
[clojure.string :as cstr]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.util :as util]
[cljam.io.sam.util :as sam-util]))

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4 changes: 2 additions & 2 deletions test/cljam/io/t_sam.clj → test/cljam/io/sam_test.clj
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(ns cljam.io.t-sam
(ns cljam.io.sam-test
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.sam :as sam]
[cljam.util :as util]))

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4 changes: 2 additions & 2 deletions test/cljam/io/t_sequence.clj → test/cljam/io/sequence_test.clj
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(ns cljam.io.t-sequence
(ns cljam.io.sequence-test
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[clojure.string :as cstr]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.fasta.core :as fa-core]
[cljam.io.sequence :as cseq]
[cljam.util :as util]))
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4 changes: 2 additions & 2 deletions test/cljam/io/t_tabix.clj → test/cljam/io/tabix_test.clj
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(ns cljam.io.t-tabix
(ns cljam.io.tabix-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.tabix :as tbi]))

(deftest about-read-index-with-error
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2 changes: 1 addition & 1 deletion test/cljam/io/util/t_cigar.clj → test/cljam/io/util/cigar_test.clj
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(ns cljam.io.util.t-cigar
(ns cljam.io.util.cigar-test
(:require [clojure.test :refer :all]
[cljam.io.util.cigar :as cgr]))

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4 changes: 2 additions & 2 deletions test/cljam/io/util/t_lsb.clj → test/cljam/io/util/lsb_test.clj
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(ns cljam.io.util.t-lsb
(ns cljam.io.util.lsb-test
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :as common]
[cljam.test-common :as common]
[cljam.io.util.lsb :as lsb])
(:import [java.nio ByteBuffer ByteOrder]
[java.io RandomAccessFile DataInputStream FileInputStream]
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4 changes: 2 additions & 2 deletions test/cljam/io/t_util.clj → test/cljam/io/util_test.clj
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(ns cljam.io.t-util
(ns cljam.io.util-test
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.util :as util]
[cljam.io.bed :as bed]
[cljam.io.fastq :as fastq]
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4 changes: 2 additions & 2 deletions test/cljam/io/vcf/t_util.clj → test/cljam/io/vcf/util_test.clj
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(ns cljam.io.vcf.t-util
(ns cljam.io.vcf.util-test
(:require [clojure.test :refer :all]
[clojure.string :as cstr]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.vcf.util :as vcf-util]))

(deftest about-parse-info
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4 changes: 2 additions & 2 deletions test/cljam/io/vcf/t_writer.clj → test/cljam/io/vcf/writer_test.clj
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(ns cljam.io.vcf.t-writer
(ns cljam.io.vcf.writer-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.vcf.writer :as vcf-writer]))

(deftest stringify-meta-info-pedigree
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4 changes: 2 additions & 2 deletions test/cljam/io/t_vcf.clj → test/cljam/io/vcf_test.clj
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(ns cljam.io.t-vcf
(ns cljam.io.vcf-test
(:require [clojure.test :refer :all]
[clojure.java.io :as cio]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[cljam.io.vcf :as vcf]
[cljam.util :as util])
(:import bgzf4j.BGZFException))
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2 changes: 1 addition & 1 deletion test/cljam/t_common.clj → test/cljam/test_common.clj
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(ns cljam.t-common
(ns cljam.test-common
(:require [digest]
[clojure.java.io :refer [file]]
[clojure.tools.logging :refer [*logger-factory*]]
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4 changes: 2 additions & 2 deletions test/cljam/tools/t_cli.clj → test/cljam/tools/cli_test.clj
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(ns cljam.tools.t-cli
(ns cljam.tools.cli-test
(:require [clojure.test :refer :all]
[cljam.t-common :refer :all]
[cljam.test-common :refer :all]
[clojure.java.io :as cio]
[cljam.tools.cli :as cli]
[cljam.io.sam :as sam])
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2 changes: 1 addition & 1 deletion test/cljam/util/t_chromosome.clj → test/cljam/util/chromosome_test.clj
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(ns cljam.util.t-chromosome
(ns cljam.util.chromosome-test
(:require [clojure.test :refer :all]
[cljam.util.chromosome :as chr]))

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2 changes: 1 addition & 1 deletion test/cljam/util/t_whole_genome.clj → test/cljam/util/whole_genome_test.clj
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(ns cljam.util.t-whole-genome
(ns cljam.util.whole-genome-test
(:require [clojure.test :refer :all]
[cljam.util.whole-genome :as wg]))

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2 changes: 1 addition & 1 deletion test/cljam/t_util.clj → test/cljam/util_test.clj
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(ns cljam.t-util
(ns cljam.util-test
"Tests for cljam.util."
(:require [clojure.test :refer :all]
[cljam.util :as util]))
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