/
merge.go
162 lines (137 loc) · 4.24 KB
/
merge.go
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package cmd
import (
"bytes"
"flag"
"fmt"
"log"
"os"
"path/filepath"
"runtime"
"strings"
"github.com/exascience/elprep/internal"
"github.com/exascience/elprep/sam"
)
// MergeHelp is the help string for this command.
const MergeHelp = "Merge parameters:\n" +
"elprep merge /path/to/input sam-output-file\n" +
"[--single-end]\n" +
"[--nr-of-threads n]\n" +
"[--reference-t fai-file]\n" +
"[--reference-T fasta-file]\n"
// Merge implements the elprep merge command.
func Merge() error {
var (
referenceFai, referenceFasta string
nrOfThreads int
singleEnd bool
)
var flags flag.FlagSet
flags.BoolVar(&singleEnd, "single-end", false, "when splitting single-end data")
flags.IntVar(&nrOfThreads, "nr-of-threads", 0, "number of worker threads")
flags.StringVar(&referenceFai, "reference-t", "", "specify a .fai file for cram output")
flags.StringVar(&referenceFasta, "reference-T", "", "specify a .fasta file for cram output")
if len(os.Args) < 4 {
fmt.Fprintln(os.Stderr, "Incorrect number of parameters.")
fmt.Fprint(os.Stderr, MergeHelp)
os.Exit(1)
}
input := getFilename(os.Args[2], MergeHelp)
output := getFilename(os.Args[3], MergeHelp)
if err := flags.Parse(os.Args[4:]); err != nil {
x := 0
if err != flag.ErrHelp {
fmt.Fprintln(os.Stderr, err)
x = 1
}
fmt.Fprint(os.Stderr, MergeHelp)
os.Exit(x)
}
setLogOutput()
// sanity checks
var sanityChecksFailed bool
referenceFai, referenceFasta, success := checkCramOutputOptions(filepath.Ext(output), referenceFai, referenceFasta)
sanityChecksFailed = !success
fullInputPath, err := internal.FullPathname(input)
if err != nil {
return err
}
filesToMerge, err := internal.Directory(fullInputPath)
if err != nil {
log.Printf("Given directory %v causes error %v.\n", input, err)
sanityChecksFailed = true
} else if len(filesToMerge) < 2 && !singleEnd {
log.Printf("Given directory %v does not contain /splits/ directory and/or spread reads file. These should have been created by an elprep split invocation.\n", input)
sanityChecksFailed = true
}
if nrOfThreads < 0 {
sanityChecksFailed = true
log.Println("Error: Invalid nr-of-threads: ", nrOfThreads)
}
if sanityChecksFailed {
fmt.Fprint(os.Stderr, MergeHelp)
os.Exit(1)
}
firstFile, err := sam.Open(filepath.Join(fullInputPath, filesToMerge[0]), true)
if err != nil {
return err
}
header, _, err := sam.ParseHeader(firstFile.Reader)
if err != nil {
return err
}
err = firstFile.Close()
if err != nil {
return err
}
var inputPrefix string
for _, file := range filesToMerge {
if idx := strings.LastIndex(file, "-unmapped"); idx >= 0 {
inputPrefix = file[:idx]
break
}
}
var inputExtension string
switch ext := filepath.Ext(filesToMerge[0]); ext {
case sam.SamExt, sam.BamExt, sam.CramExt:
inputExtension = ext[1:]
default:
inputExtension = "sam"
}
// building output command line
var command bytes.Buffer
fmt.Fprint(&command, os.Args[0], " merge ", input, " ", output)
if singleEnd {
fmt.Fprint(&command, " --single-end ")
}
if nrOfThreads > 0 {
runtime.GOMAXPROCS(nrOfThreads)
fmt.Fprint(&command, " --nr-of-threads ", nrOfThreads)
}
if referenceFai != "" {
fmt.Fprint(&command, " --reference-t ", referenceFai)
}
if referenceFasta != "" {
fmt.Fprint(&command, " --reference-T ", referenceFasta)
}
// executing command
log.Println("Executing command:\n", command.String())
output, err = internal.FullPathname(output)
if err != nil {
return err
}
switch header.HDSO() {
case sam.Coordinate:
if singleEnd {
return sam.MergeSingleEndFilesSplitPerChromosome(fullInputPath, output, referenceFai, referenceFasta, inputPrefix, inputExtension, header)
}
return sam.MergeSortedFilesSplitPerChromosome(fullInputPath, output, referenceFai, referenceFasta, inputPrefix, inputExtension, header)
case sam.Queryname:
log.Fatal("Merging of files sorted by queryname not yet implemented.")
panic("Unreachable code.")
default:
if singleEnd {
return sam.MergeSingleEndFilesSplitPerChromosome(fullInputPath, output, referenceFai, referenceFasta, inputPrefix, inputExtension, header)
}
return sam.MergeUnsortedFilesSplitPerChromosome(fullInputPath, output, referenceFai, referenceFasta, inputPrefix, inputExtension, header)
}
}