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seanlaidlaw/iRODS-Downloader

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Showing 87 of 87 total issues

don't use underscores in Go names; var attribute_with_sample_name should be attributeWithSampleName
Open

    attribute_with_sample_name := viper.GetString("attribute_with_sample_name")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var realignment_map should be realignmentMap
Open

        realignment_map := make(map[string]string)
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var job_err should be jobErr
Open

        job_err := "E_Counts_matrix_RNA/featurecounts_run.e"
Severity: Minor
Found in irods_downloader.go by golint

2: cannot find package "github.com/spf13/viper" in any of:
Open

    "github.com/spf13/viper"
Severity: Minor
Found in irods_downloader.go by govet

don't use underscores in Go names; var bam_filename should be bamFilename
Open

    bam_filename := cram.Realigned_bam_path
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var star_genome_dir should be starGenomeDir
Open

    star_genome_dir := viper.GetString("star_genome_dir")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var sample_names_map should be sampleNamesMap
Open

        sample_names_map := make(map[string][]string)
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var out_folder should be outFolder
Open

                out_folder := "D_realignments/" + strings.ReplaceAll(cram.Library_type, " ", "_") + "/"
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var matrix_out should be matrixOut
Open

        matrix_out := "E_Counts_matrix_RNA/featurecounts_matrix.tsv"
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; func quickcheck_alignments should be quickcheckAlignments
Open

func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var star_align_libraries should be starAlignLibraries
Open

    star_align_libraries := viper.GetStringSlice("star_align_libraries")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var split_filename should be splitFilename
Open

            split_filename := strings.Split(filename, "_")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var func_cram should be funcCram
Open

            func_cram := &((*cram_list)[i])
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; func parameter samtools_exec should be samtoolsExec
Open

func quickcheck_alignments(cram_list []cram_file, i int, samtools_exec string) {
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; func parameter cram_list should be cramList
Open

func indexBam(cram_list []cram_file, i int, samtools_exec string) {
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field File_exists_in_irods should be FileExistsInIrods
Open

    File_exists_in_irods         bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var cram_dl_dir should be cramDlDir
Open

        cram_dl_dir := "A_iRODS_CRAM_Downloads/"
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var undownloaded_cram_map should be undownloadedCramMap
Open

        undownloaded_cram_map := make(map[string]string)
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var bam_filename should be bamFilename
Open

    bam_filename := cram.Realigned_bam_path
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var bwa_exec should be bwaExec
Open

    bwa_exec := viper.GetString("bwa_exec")
Severity: Minor
Found in irods_downloader.go by golint
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