func TestReader2(t *testing.T) {
a, _ := fastqreader.OpenFastQ("./inputs/1.fq")
set1, _ := a.ReadBarcodeSet(nil)
Check(t, set1[0].ReadInfo == "@HWI-D00684:80:HFCKCADXX:2:2113:17628:14813 1:N:0:\n", "a")
Check(t, string(set1[1].Read1) == "AGCTGCTGCTCTCTCCATGTTTTTCCTGCACTCCTTGCAGGGACCTGAATAGCATGAACTGACTTTTCCTTGACGTAGTTGCTTCGTAGGATACTTCT", "b")
set2, _ := a.ReadBarcodeSet(&set1)
Check(t, set2[0].ReadInfo == "@HWI-D00684:80:HFCKCADXX:2:2112:14227:100270 1:N:0:\n", "c")
Check(t, string(set2[1].Read1) == "CGCGGGCAGCAGCCATGGGATGCAGGACCTGCAGTCCACACATGTCACATGAATCTCCATGGAGAGGCACACAGTTCTCCCCATCTCAGCACTCTCTC", "d")
}
func TestReader(t *testing.T) {
a, b := fastqreader.OpenFastQ("./inputs/1.fq")
Check(t, a != nil, "1")
Check(t, b == nil, "2")
var ff fastqreader.FastQRecord
a.ReadOneLine(&ff)
a.ReadOneLine(&ff)
a.ReadOneLine(&ff)
Check(t, string(ff.Read1) == "CACCGCCCTAGCCAGGAGAGAAGCACTTCTTACCTGGGTTTCTTAGAGGCTTTGGCTGGCAATATTGTCAGCACCAGAGAGGACTTCTCGATGGCTGA", "a")
Check(t, string(ff.ReadQual1) == "BBBFFFFFFFFFFIIIIIFFIIIIIIIIFIIIIIFIFIFFIIFIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFF", "b")
Check(t, string(ff.Read2) == "GTGGTAGTCTCCTGTTCAGCCATCGAGAAGTCCTCTCTGGTGCTGACAATATTGCCAGCCAAAGCCTCTAAGAAACCCAGGTAAGAAGTGCTTCTCTC", "c")
Check(t, string(ff.ReadQual2) == "BBBFFFFFFFFFFIIFIIFIIIIIIIIIIIIIIIIFIIIFFFIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIFFFFFFFFBBFFFFFBBFFFFFFFF", "d")
Check(t, string(ff.Barcode10X) == "AAACAGAGAAAGAT", "e")
Check(t, string(ff.Barcode10XQual) == "BBBFFFFFFFFFFI", "f")
Check(t, string(ff.Barcode) == "CCGAACGC", "g")
Check(t, string(ff.BarcodeQual) == "BBBFFFFF", "h")
Check(t, ff.ReadInfo == "@HWI-D00684:80:HFCKCADXX:2:2113:9410:56703 1:N:0:\n", "i")
}
//TODO remove TODO's when fixing thing TODO's relate to, not long after lol
func main() {
// Use worker thread count request on cmdline, or
// all CPUs if -threads wasn't specified
numCPU := runtime.NumCPU()
if *threads < 0 {
*threads = numCPU
}
runtime.GOMAXPROCS(*threads + 2)
flag.Parse()
if _, err := os.Stat(*reads); os.IsNotExist(err) {
panic(fmt.Sprintf("File does not exist %s", *reads))
}
if _, err := os.Stat(*genome); os.IsNotExist(err) {
panic(fmt.Sprintf("Fasta file not found %s", *genome))
}
if syscall.Access(*output, 2) != nil { //is output writable
panic(fmt.Sprintf("Output directory not writable by this process %s", *output))
}
print(fmt.Sprintf("Starting lariat. Version: %s\n", __VERSION__))
fastq, err := fastqreader.OpenFastQ(*reads)
if err != nil {
panic(err)
}
print(fmt.Sprintf("Loading reference genome: %s\n", *genome))
ref := GoBwaLoadReference(*genome)
print("Reference loaded\n")
settings := GoBwaAllocSettings()
config := &RFAConfig{}
config.improper_penalty = float64(*improper_pair_penalty) * (*alignment_score_factor)
var w *bufio.Writer
barcode_num := 0
bams, err := CreateBAMs(ref, *output, *read_group, *sample_id, *positionChunkSize, *debugTags)
if err != nil {
panic(err)
}
work_to_do := make(chan *WorkUnit, 2)
//finished := make (chan bool);
stats := &RFAStats{}
stats.file = w
/* This RW lock gets Rlocked by each worker thread. Worker threads
* unlock it when they are finished and have copied their data to the
* BAM writer
*/
var worker_lock sync.RWMutex
barcode_reads = [][]fastqreader.FastQRecord{}
/* Start some workers */
for i := 0; i < *threads; i++ {
go WorkerThread(work_to_do, bams, ref, settings, config, stats, &worker_lock)
}
/* Iterate over source file, giving work to the workers */
for {
barcode_num++
if len(barcode_reads) == 0 {
barcode_reads_lock.Lock()
barcode_reads = append(barcode_reads, make([]fastqreader.FastQRecord, 0, 50000))
barcode_reads_lock.Unlock()
}
barcode_reads_lock.Lock()
bc_reads := barcode_reads[len(barcode_reads)-1]
//fmt.Println(len(barcode_reads))
barcode_reads = barcode_reads[0 : len(barcode_reads)-1]
barcode_reads_lock.Unlock()
bc_reads, err, full_barcode := fastq.ReadBarcodeSet(&bc_reads)
if err != nil {
break
}
// Max BCs to process
if barcode_num == *max_bcs {
break
}
work_to_do <- &WorkUnit{bc_reads, barcode_num, full_barcode}
}
/* Tell each worker to exit */
for i := 0; i < *threads; i++ {
work_to_do <- nil
}
/* Wait for each worker to finish any final tasks and exit */
worker_lock.Lock()
worker_lock.Unlock()
/* Close and flush the BAM file */
bams.Close()
fmt.Println("Lariat completed successfully")
}
