sam_filter.go

package main

import (
	"bufio"
	"fmt"
	"log"
	"os"
	"sort"
	"strconv"
	"strings"
)

type Data struct {
	quality int
	rname   string
}

func main() {
	if len(os.Args) != 2 {
		log.Fatal("   Invalid command-line args. Correct Usage:\n./sam_filter /path/to/.sam > outputfile.txt")
	}

	filename := os.Args[1]

	best := getBest(filename)
	rnames := getRnameNumbers(best)
	outputRnameNumbers(rnames)
}

func getBest(filename string) map[string]Data {
	file, err := os.Open(filename)
	if err != nil {
		log.Fatal(err)
	}
	defer file.Close()

	ties := make(map[string]bool)
	uniques := make(map[string]map[int]string)
	best := make(map[string]Data)

	scanner := bufio.NewScanner(file)
	for scanner.Scan() {
		line := scanner.Text()

		// Ignore header
		if !strings.HasPrefix(line, "@") {
			fields := strings.Split(line, "\t")
			quality, _ := strconv.Atoi(fields[4])

			// If qname not in ties
			if !ties[fields[0]] {

				// If a qname with a quality has occurred > 1 time
				if _, ok := uniques[fields[0]]; !ok {
					uniques[fields[0]] = make(map[int]string)
				}
				if _, ok := uniques[fields[0]][quality]; ok {
					ties[fields[0]] = true
					delete(uniques, fields[0])
					delete(best, fields[0])
					// qname with quality is unique
				} else {
					uniques[fields[0]][quality] = fields[2]

					// If qname in best
					if val, ok := best[fields[0]]; ok {
						// If current quality > previous best quality
						if quality > val.quality {
							best[fields[0]] = Data{quality, fields[2]}
						}
						// If qname is not in bests, just write current qname, quality, and rname
					} else {
						best[fields[0]] = Data{quality, fields[2]}
					}
				}
			}
		}
	}

	return best
}

func getRnameNumbers(best map[string]Data) map[string]int {
	rnames := make(map[string]int)

	for _, val := range best {
		if _, ok := rnames[val.rname]; ok {
			rnames[val.rname] += 1
		} else {
			rnames[val.rname] = 1
		}
	}

	return rnames
}

func outputRnameNumbers(rnames map[string]int) {
	numberMap := make(map[int][]string)
	numbers := make([]int, len(rnames))

	for key, val := range rnames {
		numbers = append(numbers, val)
		numberMap[val] = append(numberMap[val], key)
	}

	sort.Sort(sort.Reverse(sort.IntSlice(numbers)))

	out := ""
	for _, num := range numbers {
		for _, rname := range numberMap[num] {
			out += rname + "\t" + strconv.Itoa(num) + "\n"
		}
	}

	fmt.Println(out)
}