/
intervalQuery.go
88 lines (79 loc) · 2.23 KB
/
intervalQuery.go
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package main
import (
"io"
"sync"
"github.com/vertgenlab/gonomics/interval"
)
type Settings struct { // Draft of input setting struct
Input string // implemented
Output string // implemented
SelectFile string // implemented
Extend int
NonOverlap bool // implemented // not compatible with MergedOutput
Threads int // implemented
PercentOverlap float64
BaseOverlap int
Aggregate bool // implemented
Relationship string // implemented
MergedOutput bool // implemented // not compatible with NonOverlap
SwapTargetQuery bool
}
type queryAnswer struct {
query interval.Interval
answer []interval.Interval
}
type fileWriter interface {
WriteToFileHandle(io.Writer)
}
func buildTree(intervals []interval.Interval, aggregate bool) map[string]*interval.IntervalNode {
if aggregate {
interval.MergeIntervals(intervals)
}
return interval.BuildTree(intervals)
}
func queryWorker(tree map[string]*interval.IntervalNode, queryChan <-chan interval.Interval, answerChan chan<- *queryAnswer, relationship string, wg *sync.WaitGroup, mergedOutput bool) {
var answer []interval.Interval
answerTrue := make([]interval.Interval, 1)
buf := make([]interval.Interval, 1000)
numSeen := 0
for query := range queryChan {
numSeen++
if mergedOutput {
answer = interval.Query(tree, query, relationship)
answerChan <- &queryAnswer{query, answer}
continue
}
// else if no merged output
if interval.QueryBool(tree, query, relationship, buf) {
answer = answerTrue
answerChan <- &queryAnswer{query, answer}
} else {
answer = nil
}
}
wg.Done()
}
func writeToFile(answerChan <-chan *queryAnswer, outfile io.Writer, mergedOutput bool, nonoverlap bool) {
if mergedOutput {
for val := range answerChan {
if len(val.answer) != 0 {
val.query.(fileWriter).WriteToFileHandle(outfile)
for _, curr := range val.answer {
curr.(fileWriter).WriteToFileHandle(outfile)
}
}
}
} else if nonoverlap {
for val := range answerChan {
if len(val.answer) == 0 {
val.query.(fileWriter).WriteToFileHandle(outfile)
}
}
} else {
for val := range answerChan {
if len(val.answer) != 0 {
val.query.(fileWriter).WriteToFileHandle(outfile)
}
}
}
}