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- added base quality score recalibration (BQSR) - added optical duplicate marking - added metrics (MultiQC compatible) - support for SAM File Format version 1.6 - support for FASTA and VCF files - support for BAM/BGZF files - support for elPrep-specific elsites and elfasta formats - split/filter/merge (sfm) mode now implemented in Go instead of Python - added --log-path option to all tools - various API and performance improvements - changed license to the GNU Affero General Public License version 3 as published by the Free Software Foundation, with Additional Terms - updated demos
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| // elPrep: a high-performance tool for preparing SAM/BAM files. | ||
| // Copyright (c) 2017, 2018 imec vzw. | ||
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| // This program is free software: you can redistribute it and/or modify | ||
| // it under the terms of the GNU Affero General Public License as | ||
| // published by the Free Software Foundation, either version 3 of the | ||
| // License, or (at your option) any later version, and Additional Terms | ||
| // (see below). | ||
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| // This program is distributed in the hope that it will be useful, but | ||
| // WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| // Affero General Public License for more details. | ||
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| // You should have received a copy of the GNU Affero General Public | ||
| // License and Additional Terms along with this program. If not, see | ||
| // <https://github.com/ExaScience/elprep/blob/master/LICENSE.txt>. | ||
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| package cmd | ||
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| import ( | ||
| "flag" | ||
| "fmt" | ||
| "os" | ||
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| "github.com/exascience/elprep/v4/fasta" | ||
| "github.com/exascience/elprep/v4/intervals" | ||
| ) | ||
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| // VcfToElsitesHelp is the help string for this command. | ||
| const VcfToElsitesHelp = "vcf-to-elsites parameters:\n" + | ||
| "elprep vcf-to-elsites vcf-file elsites-file\n" + | ||
| "[--log-path path]\n" | ||
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| // VcfToElsites implements the elprep vcf-to-elsites command. | ||
| func VcfToElsites() error { | ||
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| var logPath string | ||
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| var flags flag.FlagSet | ||
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| flags.StringVar(&logPath, "log-path", "", "write log files to the specified directory") | ||
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| var input, output string | ||
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| if len(os.Args) < 4 { | ||
| fmt.Fprintln(os.Stderr, "Incorrect number of parameters.") | ||
| fmt.Fprint(os.Stderr, VcfToElsitesHelp) | ||
| os.Exit(1) | ||
| } | ||
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| input = getFilename(os.Args[2], VcfToElsitesHelp) | ||
| output = getFilename(os.Args[3], VcfToElsitesHelp) | ||
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| setLogOutput(logPath) | ||
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| inter, err := intervals.FromVcfFile(input) | ||
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| if err != nil { | ||
| return err | ||
| } | ||
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| for chrom, ivals := range inter { | ||
| intervals.ParallelSortByStart(ivals) | ||
| inter[chrom] = intervals.ParallelFlatten(ivals) | ||
| } | ||
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| return intervals.ToElsitesFile(inter, output) | ||
| } | ||
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| // BedToElsitesHelp is the help string for this command. | ||
| const BedToElsitesHelp = "\nbed-to-elsites parameters:\n" + | ||
| "elprep bed-to-elsites bed-file elsites-file\n" + | ||
| "[--log-path path]\n" | ||
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| // BedToElsites implements the elprep bed-to-elsites command. | ||
| func BedToElsites() error { | ||
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| var logPath string | ||
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| var flags flag.FlagSet | ||
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| flags.StringVar(&logPath, "log-path", "", "write log files to the specified directory") | ||
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| parseFlags(flags, 4, BedToElsitesHelp) | ||
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| input := getFilename(os.Args[2], BedToElsitesHelp) | ||
| output := getFilename(os.Args[3], BedToElsitesHelp) | ||
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| setLogOutput(logPath) | ||
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| inter, err := intervals.FromBedFile(input) | ||
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| if err != nil { | ||
| return err | ||
| } | ||
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| for chrom, ivals := range inter { | ||
| intervals.ParallelSortByStart(ivals) | ||
| inter[chrom] = intervals.ParallelFlatten(ivals) | ||
| } | ||
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| return intervals.ToElsitesFile(inter, output) | ||
| } | ||
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| // FastaToElfastaHelp is the help string for this command. | ||
| const FastaToElfastaHelp = "fasta-to-elfasta parameters:\n" + | ||
| "elprep fasta-to-elfasta fasta-file elfasta-file\n" + | ||
| "[--log-path path]\n" | ||
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| // FastaToElfasta implements the elprep fasta-to-elfasta command. | ||
| func FastaToElfasta() error { | ||
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| var logPath string | ||
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| var flags flag.FlagSet | ||
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| flags.StringVar(&logPath, "log-path", "", "write log files to the specified directory") | ||
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| var input, output string | ||
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| if len(os.Args) < 4 { | ||
| fmt.Fprintln(os.Stderr, "Incorrect number of parameters.") | ||
| fmt.Fprintln(os.Stderr, FastaToElfastaHelp) | ||
| os.Exit(1) | ||
| } | ||
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| input = getFilename(os.Args[2], FastaToElfastaHelp) | ||
| output = getFilename(os.Args[3], FastaToElfastaHelp) | ||
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| setLogOutput(logPath) | ||
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| fst, err := fasta.ParseFasta(input, nil, false, false) | ||
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| if err != nil { | ||
| return err | ||
| } | ||
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| return fasta.ToElfasta(fst, output) | ||
| } |
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