-
Notifications
You must be signed in to change notification settings - Fork 40
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Added --tmp-path option for sfm. * Fixed /dev/stdin and /dev/stdout for sfm. * Added a command for merging intermediate metrics files. * Fixed detection of directory path names in sfm.
- Loading branch information
Showing
12 changed files
with
262 additions
and
41 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| // elPrep: a high-performance tool for preparing SAM/BAM files. | ||
| // Copyright (c) 2017-2019 imec vzw. | ||
|
|
||
| // 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). | ||
|
|
||
| // 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. | ||
|
|
||
| // 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>. | ||
|
|
||
| package cmd | ||
|
|
||
| import ( | ||
| "bytes" | ||
| "flag" | ||
| "fmt" | ||
| "log" | ||
| "os" | ||
| "path/filepath" | ||
| "runtime" | ||
|
|
||
| "github.com/exascience/elprep/v4/filters" | ||
| ) | ||
|
|
||
| // MergeOpticalDuplicatesMetricsHelp is the help string for this command. | ||
| const MergeOpticalDuplicatesMetricsHelp = "\nmerge-optical-duplicates-metrics parameters:\n" + | ||
| "elprep merge-optical-duplicates-metrics sam-input-file sam-output-file metrics-file /path/to/intermediate/metrics\n" + | ||
| "[--remove-duplicates]\n" + | ||
| "[--nr-of-threads nr]\n" + | ||
| "[--timed]\n" + | ||
| "[--log-path path]\n" | ||
|
|
||
| // Merge implements the elprep merge command. | ||
| func MergeOpticalDuplicatesMetrics() error { | ||
| var ( | ||
| profile, logPath string | ||
| nrOfThreads int | ||
| timed, removeDuplicates bool | ||
| ) | ||
|
|
||
| var flags flag.FlagSet | ||
|
|
||
| flags.IntVar(&nrOfThreads, "nr-of-threads", 0, "number of worker threads") | ||
| flags.BoolVar(&timed, "timed", false, "measure the runtime") | ||
| flags.BoolVar(&removeDuplicates, "remove-duplicates", false, "use when duplicates were removed during duplicate marking") | ||
| flags.StringVar(&profile, "profile", "", "write a runtime profile to the specified file(s)") | ||
| flags.StringVar(&logPath, "log-path", "", "write log files to the specified directory") | ||
|
|
||
| parseFlags(flags, 6, MergeOpticalDuplicatesMetricsHelp) | ||
|
|
||
| input := getFilename(os.Args[2], MergeOpticalDuplicatesMetricsHelp) | ||
| output := getFilename(os.Args[3], MergeOpticalDuplicatesMetricsHelp) | ||
| metrics := getFilename(os.Args[4], MergeOpticalDuplicatesMetricsHelp) | ||
| intermediateMetrics := getFilename(os.Args[5], MergeOpticalDuplicatesMetricsHelp) | ||
|
|
||
| setLogOutput(logPath) | ||
|
|
||
| // sanity checks | ||
|
|
||
| var sanityChecksFailed bool | ||
|
|
||
| if !checkExist("", input) { | ||
| log.Println("Warning: Input file does not exist: ", input) | ||
| } | ||
|
|
||
| if !checkExist("", intermediateMetrics) { | ||
| sanityChecksFailed = true | ||
| } | ||
|
|
||
| if profile != "" && !checkCreate("--profile", profile) { | ||
| sanityChecksFailed = true | ||
| } | ||
|
|
||
| metricsDir, err := filepath.Abs(intermediateMetrics) | ||
| if err != nil { | ||
| return err | ||
| } | ||
|
|
||
| if nrOfThreads < 0 { | ||
| sanityChecksFailed = true | ||
| log.Println("Error: Invalid nr-of-threads: ", nrOfThreads) | ||
| } | ||
|
|
||
| if sanityChecksFailed { | ||
| fmt.Fprint(os.Stderr, MergeOpticalDuplicatesMetricsHelp) | ||
| os.Exit(1) | ||
| } | ||
|
|
||
| // building output command line | ||
|
|
||
| var command bytes.Buffer | ||
| fmt.Fprint(&command, os.Args[0], " merge-optical-duplicates-metrics ", input, " ", output, " ", metrics, " ", intermediateMetrics) | ||
| if nrOfThreads > 0 { | ||
| runtime.GOMAXPROCS(nrOfThreads) | ||
| fmt.Fprint(&command, " --nr-of-threads ", nrOfThreads) | ||
| } | ||
| if timed { | ||
| fmt.Fprint(&command, " --timed ") | ||
| } | ||
| if logPath != "" { | ||
| fmt.Fprint(&command, " --log-path ", logPath) | ||
| } | ||
| if removeDuplicates { | ||
| fmt.Fprint(&command, " --remove-duplicates") | ||
| } | ||
|
|
||
| // executing command | ||
|
|
||
| log.Println("Executing command:\n", command.String()) | ||
|
|
||
| var ctr filters.DuplicatesCtrMap | ||
|
|
||
| // merge intermediate metrics files | ||
| err = timedRun(timed, profile, "Loading and combining duplicate metrics.", 1, func() error { | ||
| ctr = filters.LoadAndCombineDuplicateMetrics(metricsDir) | ||
| return ctr.Err() | ||
| }) | ||
| if err != nil { | ||
| return err | ||
| } | ||
| return timedRun(timed, profile, "Printing comdined duplicate metrics.", 2, func() error { | ||
| return filters.PrintDuplicatesMetrics(input, output, metrics, removeDuplicates, ctr) | ||
| }) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.