func writeIndex(sexes map[string][]float64, counts []*counter, samples []string, directory string, pca8 [][]uint8, slopes []float32,
	chromNames []string, mapped []uint64, unmapped []uint64) string {
	if len(sexes) == 0 {
		log.Println("sex chromosomes not found.")
	}
	pcs, pcaPlots, pcajs := pca(pca8, samples)
	binChart, binjs := plotBins(counts, samples)
	sexes["_inferred"] = make([]float64, len(samples))
	f, err := os.Create(fmt.Sprintf("%s.ped", getBase(directory)))
	if err != nil {
		panic(err)
	}
	defer f.Close()
	hdr := make([]string, len(sexes)-1, len(sexes)+7)
	keys := make([]string, 0, len(sexes))
	for k := range sexes {
		if k == "_inferred" {
			continue
		}
		keys = append(keys, k)
	}
	sort.Strings(keys)
	for i, k := range keys {
		hdr[i] = "CN" + k
	}
	hdr = append(hdr, []string{"bins.out", "bins.lo", "bins.hi", "bins.in", "slope", "p.out"}...)
	var c int
	if pcs != nil {
		_, c = pcs.Dims()
		for i := 0; i < 5 && i < c; i++ {
			hdr = append(hdr, fmt.Sprintf("PC%d", i+1))
		}
	}
	if mapped != nil {
		hdr = append(hdr, "mapped")
		hdr = append(hdr, "unmapped")
	}
	fmt.Fprintf(f, "#family_id\tsample_id\tpaternal_id\tmaternal_id\tsex\tphenotype\t%s\n", strings.Join(hdr, "\t"))
	tmpl := "unknown\t%s\t-9\t-9\t%d\t-9\t"
	var inferred int
	for i, s := range samples {
		if counts[i] == nil {
			continue
		}
		if len(sexes) > 1 {  
			inferred = int(0.5 + sexes[keys[0]][i])
		} else {
			inferred = -9
		}
		fmt.Fprintf(f, tmpl, s, inferred)
		sexes["_inferred"][i] = float64(inferred)
		s := make([]string, 0, len(keys)+4)
		for _, k := range keys {
			if _, ok := sexes[k]; ok {
				s = append(s, fmt.Sprintf("%.2f", sexes[k][i]))
			} else {
				s = append(s, "-9")
			}
		}
		cnt := counts[i]
		s = append(s, []string{
			fmt.Sprintf("%d", cnt.out),
			fmt.Sprintf("%d", cnt.low),
			fmt.Sprintf("%d", cnt.hi),
			fmt.Sprintf("%d", cnt.in),
			fmt.Sprintf("%.3f", slopes[i]),
			fmt.Sprintf("%.2f", float64(cnt.out)/float64(cnt.in)),
		}...)
		for j := 0; j < c && j < 5; j++ {
			s = append(s, fmt.Sprintf("%.2f", pcs.At(i, j)))
		}
		if mapped != nil {
			s = append(s, strconv.Itoa(int(mapped[i])))
			s = append(s, strconv.Itoa(int(unmapped[i])))
		}
		fmt.Fprintln(f, strings.Join(s, "\t"))
	}
	var sexChart *chartjs.Chart
	var sexjs string
	if len(keys) > 1 && len(sexes) > 1 {
		sexChart, sexjs, err = plotSex(sexes, keys[:2], samples)
		if err != nil {
			panic(err)
		}
	}
	var mapChart *chartjs.Chart
	var mapjs string
	if mapped != nil {
		mapChart, mapjs, err = plotMapped(mapped, unmapped, samples)
		if err != nil {
			panic(err)
		}
	}
	indexPath := fmt.Sprintf("%s%cindex.html", directory, os.PathSeparator)
	wtr, err := os.Create(indexPath)
	if err != nil {
		panic(err)
	}
	if sexChart != nil {
		asPng(fmt.Sprintf("%s-sex.png", getBase(directory)), *sexChart, 6, 6)
	}
	chartMap := map[string]interface{}{"pcajs": template.JS(pcajs), "pcbjs": template.JS(pcajs),
		"template": chartTemplate,
		"sex":    sexChart,
		"hasSex": sexChart != nil,
		"sexjs":  template.JS(sexjs),
		"mapChart": mapChart,
		"hasMap":   mapped != nil,
		"mapjs":    template.JS(mapjs),
		"bin":     binChart,
		"binjs":   template.JS(binjs),
		"version": goleft.Version,
		"prefix":  getBase(directory),
		"name":    filepath.Base(directory),
		"chroms":  chromNames}
	if len(pcaPlots) > 1 {
		chartMap["pca"] = pcaPlots[0]
		chartMap["pcb"] = pcaPlots[1]
		chartMap["hasPCA"] = true
	} else {
		chartMap["hasPCA"] = false
	}
	chartMap["notmany"] = len(samples) <= maxSamples
	if err := chartjs.SaveCharts(wtr, chartMap, chartjs.Chart{}); err != nil {
		panic(err)
	}
	wtr.Close()
	return indexPath
}
write an index.html and a ped file. includes the PC projections and inferred sexes.
package indexcov
import (
	"bufio"
	"compress/gzip"
	"fmt"
	"html/template"
	"io"
	"log"
	"os"
	"os/exec"
	"path/filepath"
	"reflect"
	"regexp"
	"sort"
	"strconv"
	"strings"
	"sync"
	"time"
	"gonum.org/v1/gonum/floats"
	"gonum.org/v1/gonum/mat"
	"gonum.org/v1/gonum/stat"
	arg "github.com/alexflint/go-arg"
	"github.com/biogo/biogo/io/seqio/fai"
	"github.com/biogo/hts/bam"
	"github.com/biogo/hts/bgzf"
	"github.com/biogo/hts/sam"
	chartjs "github.com/brentp/go-chartjs"
	"github.com/brentp/go-chartjs/types"
	"github.com/brentp/goleft"
	"github.com/brentp/goleft/indexcov/crai"
	"github.com/brentp/xopen"
)
var Ploidy = 2
var cli = &struct {
	Directory      string         `arg:"-d,required,help:directory for output files"`
	IncludeGL      bool           `arg:"-e,help:plot GL chromosomes like: GL000201.1 which are not plotted by default"`
	ExcludePatt    string         `arg:-p,help:regular expression of chromosome names to exclude"`
	Sex            string         `arg:"-X,help:comma delimited names of the sex chromosome(s) used to infer sex. Set to '' if no sex chromosomes are present."`
	Chrom          string         `arg:"-c,help:optional chromosome to extract depth. default is entire genome."`
	Fai            string         `arg:"-f,help:fasta index file. Required when crais are used."`
	ExtraNormalize bool           `arg:"-n,help:normalize across samples and do local smoothign within sample. this is recommended for CRAI"`
	Bam            []string       `arg:"positional,required,help:bam(s) or crais for which to estimate coverage"`
	sex            []string       `arg:"-"`
	exclude        *regexp.Regexp `arg:"-"`
}{Sex: "X,Y", ExcludePatt: `^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d$`}
// MaxCN is the maximum normalized value.
var MaxCN = float32(8)
// Index wraps a bam.Index to cache calculated values.
type Index struct {
	*bam.Index
	crai *crai.Index
	path string
	//mu                *sync.RWMutex
	medianSizePerTile float64
	sizes             [][]int64
	mapped            uint64
	unmapped          uint64
}
func (i *Index) Path() string {
	return i.path
}
// Sizes returns the size of each block in slices of chromosomes.
func (i *Index) Sizes() [][]int64 {
	return i.sizes
}
func vOffset(o bgzf.Offset) int64 {
	return o.File<<16 | int64(o.Block)
}
// init sets the medianSizePerTile
func (x *Index) init() {
	if x.Index != nil {
		x.sizes, x.mapped, x.unmapped = getSizes(x.Index)
		x.Index = nil
	} else if x.crai != nil {
		x.sizes = x.crai.Sizes()
		if x.sizes == nil {
			log.Fatal("bad index:", x.path)
		}
		x.crai = nil
	}
	// sizes is used to get the median.
	sizes := make([]int64, 0, 16384)
	for k := 0; k < len(x.sizes); k++ {
		sizes = append(sizes, x.sizes[k]...)
	}
	if len(sizes) < 1 {
		log.Fatalf("indexcov: no usable chromsomes in bam: %s", x.path)
	}
	sort.Slice(sizes, func(i, j int) bool { return sizes[i] < sizes[j] })
	total := int64(0)
	cumsum := make([]int64, len(sizes))
	// some bins with very high coverage can screw the normalization.
	// so we cap at the 98th percentile and then take the bin that passed then
	// median.
	n98 := sizes[int(0.98*float64(len(sizes)))]
	for i, s := range sizes {
		if s > n98 {
			s = n98
		}
		total += s
		cumsum[i] = total
	}
	var idx = sort.Search(len(cumsum), func(i int) bool { return (cumsum[i]) > (total / 2) })
	for idx >= len(sizes) {
		idx--
	}
	x.medianSizePerTile = float64(sizes[idx])
}
// NormalizedDepth returns a list of numbers for the normalized depth of the given region.
// Values are scaled to have a mean of 1. If end is 0, the full chromosome is returned.
func (x *Index) NormalizedDepth(refID int) []float32 {
	if x.medianSizePerTile == 0.0 {
		x.init()
	}
	if refID >= len(x.sizes) {
		return make([]float32, 0)
	}
	ref := x.sizes[refID]
	depths := make([]float32, 0, len(ref))
	if x.medianSizePerTile == 0 {
		return depths
	}
	for i, o := range ref {
		depths = append(depths, float32(float64(o)/x.medianSizePerTile))
		if depths[i] > 50000 {
			depths[i] = 50000
		}
	}
	return depths
}
const slots = 70
// with 0.5, we'll get centered at 1 and max of 2.
// so the max is 1/slotsMid
const slotsMid = float64(2) / float64(3)
func tint(f float32) int {
	if v := int(f); v < slots {
		if v < 0 {
			return 0
		}
		return v
	}
	return slots - 1
}
// CountsAtDepth calculates the count of items in depths that are at 100 * d
func CountsAtDepth(depths []float32, counts []int) {
	if len(counts) != slots {
		panic(fmt.Sprintf("indexcov: expecting counts to be length %d, was: %d", slots, len(counts)))
	}
	for _, d := range depths {
		counts[tint(d*(slots*float32(slotsMid))+0.5)]++
	}
}
// CountsROC returns a slice that indicates the cumulative proportion of
// 16KB chunks that were at least (normalized) depth given by their index.
func CountsROC(counts []int) []float32 {
	totals := make([]int, len(counts))
	totals[len(totals)-1] = counts[len(totals)-1]
	for i := len(totals) - 2; i >= 0; i-- {
		totals[i] = totals[i+1] + counts[i]
	}
	max := float32(totals[0])
	roc := make([]float32, len(counts))
	for i := 0; i < len(roc); i++ {
		roc[i] = float32(totals[i]) / max
	}
	return roc
}
func getRef(b *bam.Reader, chrom string) *sam.Reference {
	refs := b.Header().Refs()
	if strings.HasPrefix(chrom, "chr") {
		chrom = chrom[3:]
	}
	for _, ref := range refs {
		if chrom == ref.Name() {
			return ref
		}
		if strings.HasPrefix(ref.Name(), "chr") {
			if chrom == ref.Name()[3:] {
				return ref
			}
		}
	}
	return nil
}
func GetShortName(b string, isCrai bool) (string, error) {
	// TODO: replace this with samplename.Names()
	if !isCrai {
		fh, err := os.Open(b)
		if err != nil {
			return "", err
		}
		defer fh.Close()
		br, err := bam.NewReader(fh, 1)
		if err != nil {
			return "", err
		}
		defer br.Close()
		m := make(map[string]bool)
		for _, rg := range br.Header().RGs() {
			m[rg.Get(sam.Tag([2]byte{'S', 'M'}))] = true
		}
		if len(m) > 1 {
			return "", fmt.Errorf("bam reagroup: more than one RG for %s", b)
		}
		for sm := range m {
			return sm, nil
		}
	}
	vs := strings.Split(b, "/")
	v := vs[len(vs)-1]
	vs = strings.Split(v, ".")
	if len(vs) <= 2 {
		return vs[0], nil
	}
	v = strings.Join(vs[0:len(vs)-1], "-")
	return v, nil
}
func getWriter(base string) (*bgzf.Writer, error) {
	fh, err := os.Create(fmt.Sprintf("%s.bed.gz", base))
	if err != nil {
		return nil, err
	}
	w := bgzf.NewWriter(fh, 1)
	w.ModTime = time.Unix(0, 0)
	w.OS = 0xff
	return w, nil
}
func zero(ints []int) {
	for i := range ints {
		ints[i] = 0
	}
}
func getDirectory(path string) (bool, error) {
	fi, err := os.Stat(path)
	if err != nil {
		if err := os.MkdirAll(path, 0755); err != nil {
			return false, err
		}
		return true, nil
	}
	return fi.IsDir(), nil
}
// ReadFai returns a slit of references from the fai path.
// If chrom is "" all chromosomes are returned.
func ReadFai(path string, chrom string) []*sam.Reference {
	f, err := os.Open(path)
	if err != nil {
		fmt.Fprintf(os.Stderr, "error opening fai: %s. Is is present?\n", path)
		panic(err)
	}
	idx, err := fai.ReadFrom(f)
	if err != nil {
		fmt.Fprintf(os.Stderr, "error opening fai: %s. are you sure this i  s a valid fasta index?\n", path)
		panic(err)
	}
	recs := make([]fai.Record, 0, len(idx))
	for _, rec := range idx {
		recs = append(recs, rec)
	}
	sort.Slice(recs, func(i, j int) bool { return recs[i].Start < recs[j].Start })
	refs := make([]*sam.Reference, 0, len(idx))
	for _, rec := range recs {
		if chrom != "" && rec.Name != chrom {
			continue
		}
		ref, err := sam.NewReference(rec.Name, "", "", rec.Length, nil, nil)
		if err != nil {
			panic(err)
		}
		// add to the header so the id gets set.
		refs = append(refs, ref)
	}
	if len(refs) == 0 {
		if chrom != "" {
			log.Printf("ERROR: didn't find %s in %s", chrom, path)
		}
		panic(fmt.Sprintf("ERROR: didn't find any usable chromosomes in %s", path))
	}
	h, err := sam.NewHeader(nil, refs)
	if err != nil {
		panic(err)
	}
	return h.Refs()
}
func RefsFromBam(path string, chrom string) []*sam.Reference {
	rdr, err := os.Open(path)
	if err != nil {
		log.Println("ERROR: since no .fai was specified, expected input to be a list of bams")
		log.Printf("ERROR: got, e.g. %s", path)
		panic(err)
	}
	brdr, err := bam.NewReader(rdr, 2)
	if err != nil {
		panic(err)
	}
	refs := brdr.Header().Refs()
	if chrom != "" {
		refs = append(refs, getRef(brdr, chrom))
	}
	rdr.Close()
	brdr.Close()
	if refs == nil {
		panic(fmt.Sprintf("indexcov: chromosome: %s not found", chrom))
	}
	return refs
}
func getReferences() []*sam.Reference {
	if strings.HasSuffix(cli.Bam[0], ".bam") {
		return RefsFromBam(cli.Bam[0], cli.Chrom)
	}
	if cli.Fai != "" {
		return ReadFai(cli.Fai, cli.Chrom)
	}
	if strings.HasSuffix(cli.Bam[0], ".crai") {
		path := cli.Bam[0][:len(cli.Bam[0])-5]
		if xopen.Exists(cli.Bam[0][:len(cli.Bam[0])-5] + ".cram") {
			path = cli.Bam[0][:len(cli.Bam[0])-5] + ".cram"
		}
		if p, err := exec.LookPath("samtools"); err == nil {
			log.Println(p, "view", "-H", path)
			if out, e := exec.Command(p, "view", "-H", path).Output(); e == nil {
				if h, e := sam.NewHeader(out, nil); e == nil {
					return h.Refs()
				}
			} else {
				log.Println(e)
			}
		} else {
			log.Println(err)
			log.Fatal("indexcov: samtools is required to be on the path if indexcov is given cram indexes without an fai")
		}
	}
	return RefsFromBam(cli.Bam[0], cli.Chrom)
}
func expandGlobs(paths []string) []string {
	result := make([]string, 0, len(paths))
	for _, p := range paths {
		matches, err := filepath.Glob(p)
		if err != nil {
			log.Fatal("indexcov: error with file path:" + p + "\n" + err.Error())
		}
		for _, m := range matches {
			result = append(result, m)
		}
	}
	return result
}
// Main is called from the goleft dispatcher
func Main() {
	chartjs.XFloatFormat = "%.0f"
	p := arg.MustParse(cli)
	if len(cli.Bam) == 0 {
		p.Fail(fmt.Sprintf("indexcov: expected at least 1 bam/bai/crai: %s", os.Args))
	}
	if len(cli.Sex) > 0 {
		cli.sex = strings.Split(strings.TrimSpace(cli.Sex), ",")
	}
	if cli.ExcludePatt != "" {
		cli.exclude = regexp.MustCompile(cli.ExcludePatt)
	}
	if exists, err := getDirectory(cli.Directory); err != nil || !exists {
		log.Fatalf("indexcov: error creating specified directory: %s, %s", cli.Directory, err)
	}
	// the lengths and names of references from bams or fasta
	refs := getReferences()
	cli.Bam = expandGlobs(cli.Bam)
	names := make([]string, len(cli.Bam))
	idxs := make([]*Index, len(cli.Bam))
	ch := make(chan rdi, 8)
	wg := &sync.WaitGroup{}
	wg.Add(8)
	for k := 0; k < 8; k++ {
		go func() {
			for r := range ch {
				idx, name, i := readIndex(r)
				names[i] = name
				idxs[i] = idx
			}
			wg.Done()
		}()
	}
	for i, b := range cli.Bam {
		ch <- rdi{bamPath: b, i: i}
	}
	close(ch)
	wg.Wait()
	sexes, counts, pca8, chromNames, slopes := run(refs, idxs, names, getBase(cli.Directory), cli.ExtraNormalize)
	mapped := make([]uint64, len(names))
	unmapped := make([]uint64, len(names))
	anygt := false
	for i, ix := range idxs {
		mapped[i] = ix.mapped
		unmapped[i] = ix.unmapped
		if ix.mapped > 0 || ix.unmapped > 0 {
			anygt = true
		}
	}
	if !anygt {
		mapped = nil
		unmapped = nil
	}
	chartjs.XFloatFormat = "%.2f"
	if indexPath := writeIndex(sexes, counts, names, cli.Directory, pca8, slopes, chromNames, mapped, unmapped); indexPath != "" {
		fmt.Fprintf(os.Stderr, "indexcov finished: see %s for overview of output\n", indexPath)
	}
}
type rdi struct {
	bamPath string
	i       int
}
// ReadIndex returns an Index pointer from the specified bam or crai path.
func ReadIndex(path string) *Index {
	i, _, _ := readIndex(rdi{path, 0})
	return i
}
// get an initialized index from a bamPath.
// `i` is used in the return when parallelized to keep same order.
func readIndex(r rdi) (*Index, string, int) {
	b := r.bamPath
	if strings.HasSuffix(b, ".crai") {
		f, err := os.Open(b)
		if err != nil {
			panic(err)
		}
		gz, err := gzip.NewReader(f)
		if err != nil {
			log.Printf("error from index: %s", b)
			panic(err)
		}
		cr, err := crai.ReadIndex(gz)
		if err != nil {
			log.Printf("error from index: %s", b)
			panic(err)
		}
		idx := &Index{crai: cr, path: b}
		idx.init()
		nm, err := GetShortName(b, true)
		if err != nil {
			panic(err)
		}
		return idx, nm, r.i
	}
	suf := ".bai"
	if strings.HasSuffix(b, ".bai") {
		suf = ""
	}
	rdr, err := os.Open(b + suf)
	if err != nil {
		var terr error
		rdr, terr = os.Open(b[:(len(b)-4)] + suf)
		if terr != nil {
			panic(err)
		}
	}
	dx, err := bam.ReadIndex(bufio.NewReader(rdr))
	if err != nil {
		panic(err)
	}
	idx := &Index{Index: dx, path: b}
	idx.init()
	nm, err := GetShortName(b, strings.HasSuffix(b, ".bai"))
	if err != nil {
		panic(err)
	}
	return idx, nm, r.i
}
// if there are more samples than this then the depth plots won't be drawn.
const maxSamples = 100
func sameChrom(as []string, b string) bool {
	for _, a := range as {
		if a == b {
			return true
		}
		na := a
		if strings.HasPrefix(a, "chr") {
			na = a[3:]
		} else if strings.HasPrefix(b, "chr") {
			na = "chr" + a
		}
		if na == b {
			return true
			//log.Printf(`indexcov: found chromosome "%s", wanted "%s" please use exact chromosome names for --sex.`, b, a)
		}
	}
	return false
}
func normalizeAcrossSamples(depths [][]float32) {
	// depths is n_samples, n-sites
	if len(depths) < 5 {
		return
	}
	var maxLen = 0
	for _, d := range depths {
		if len(d) > maxLen {
			maxLen = len(d)
		}
	}
	for j := 0; j < maxLen; j++ {
		var m float64 = 0
		var n float64 = 0
		for i := range depths {
			if len(depths[i]) > j {
				// take mean of j-1:j+1 for a bit of smoothing
				m += float64(depths[i][j])
				n++
				if j > 0 {
					m += float64(depths[i][j-1])
					n++
				}
				if j < len(depths[i])-1 {
					m += float64(depths[i][j+1])
					n++
				}
			}
		}
		if int(n) < 3*len(depths)-4 {
			continue
		}
		m /= n
		if m < 0.1 {
			continue
		}
		for i := range depths {
			if len(depths[i]) > j {
				depths[i][j] /= float32(m)
				if j > 2 && j < len(depths[i])-3 {
					// i + 1 is not scaled yet, so scale it here.
					// moving average of window-size 5
					depths[i][j] = 1.0 / 7.0 * (depths[i][j-3] + depths[i][j-2] + depths[i][j-1] + depths[i][j] + depths[i][j+1]/float32(m) + depths[i][j+2]/float32(m) + depths[i][j+3]/float32(m))
				}
			}
		}
	}
}
func run(refs []*sam.Reference, idxs []*Index, names []string, base string, interSampleNormalize bool) (map[string][]float64, []*counter, [][]uint8, []string, []float32) {
	// keep a slice of charts since we plot all of the coverage roc charts in a single html file.
	sexes := make(map[string][]float64)
	counts := make([][]int, len(idxs))
	depths := make([][]float32, len(idxs))
	// slope of coverage line between 1-delta and 1+delta.
	slopes, nSlopes := make([]float32, len(idxs)), 0
	offs := make([]*counter, len(idxs))
	// uint8 to use less memory.
	pca8 := make([][]uint8, len(idxs))
	log.Printf("indexcov: running on %d indexes", len(idxs))
	if len(idxs) > maxSamples {
		log.Printf("indexcov: creating only static (no interactive) plots for depth because # of samples %d is > %d\n", len(idxs), maxSamples)
	}
	tmp, err := getWriter(base)
	if err != nil {
		panic(err)
	}
	defer tmp.Close()
	bgz := bufio.NewWriter(tmp)
	defer bgz.Flush()
	rtmp, err := os.Create(fmt.Sprintf("%s.roc", base))
	if err != nil {
		panic(err)
	}
	defer rtmp.Close()
	rfh := bufio.NewWriter(rtmp)
	defer rfh.Flush()
	chromNames := make([]string, 0, len(refs))
	fmt.Fprintf(bgz, "#chrom\tstart\tend\t%s\n", strings.Join(names, "\t"))
	ir := -1
	var nreported = 0
	for _, ref := range refs {
		chrom := ref.Name()
		if cli.exclude != nil && cli.exclude.Match([]byte(chrom)) {
			if nreported < 10 {
				log.Printf("indexcv: excluding chromosome: %s because of exclude-pattern: %s", chrom, cli.ExcludePatt)
				nreported += 1
				if nreported == 10 {
					log.Println("not reporting further skipped chromosomes")
				}
			}
			continue
		}
		ir++
		// Some samples may not have all the data, so we always take the longest sample for printing.
		longest, longesti := 0, 0
		for k, idx := range idxs {
			if ir == 0 {
				pca8[k] = make([]uint8, 0, 2e5)
				offs[k] = &counter{}
			}
			depths[k] = idx.NormalizedDepth(ref.ID())
			if len(depths[k]) > longest {
				longesti = k
				longest = len(depths[k])
			}
			if ir == 0 {
				counts[k] = make([]int, slots)
			} else {
				zero(counts[k])
			}
		}
		isSex := sameChrom(cli.sex, chrom)
		if interSampleNormalize && !isSex {
			normalizeAcrossSamples(depths)
		}
		for k := range idxs {
			CountsAtDepth(depths[k], counts[k])
		}
		for i := 0; i < len(depths[longesti]); i++ {
			fmt.Fprintf(bgz, "%s\t%d\t%d\t%s\n", chrom, i*16384, (i+1)*16384, depthsFor(depths, i))
		}
		if isSex {
			if len(depths[longesti]) > 0 {
				sexes[chrom] = GetCN(depths)
			}
		} else {
			// now add non-sex chromosomes to the pca data since we know the longest.
			var dp float32
			for k := range idxs {
				i := -1 // initalize to -1 to differentiate from never entering loop.
				dps := depths[k]
				for i, dp = range dps {
					// := depths[k][i]
					if dp > MaxCN {
						dp = MaxCN
						depths[k][i] = dp
					}
					pca8[k] = append(pca8[k], uint8(65535/MaxCN*dp+0.5))
				}
				for ; i < longest; i++ {
					pca8[k] = append(pca8[k], 0)
				}
				offs[k].count(dps, longest)
			}
		}
		if len(depths[longesti]) > 0 {
			c, rocs := writeROCs(counts, names, chrom, rfh)
			// only plot those with at least 3 regions.
			if (cli.IncludeGL || !strings.HasPrefix(chrom, "GL")) && len(depths[longesti]) > 2 {
				if !isSex && longest > 100 {
					updateSlopes(rocs, float32(ref.Len())/1e6, slopes)
					nSlopes++
				}
				chromNames = append(chromNames, chrom)
				if err := plotDepths(depths, names, chrom, base, len(names) <= maxSamples); err != nil {
					panic(err)
				}
				tmp := chartjs.XFloatFormat
				chartjs.XFloatFormat = "%.2f"
				c.Options.Legend = &chartjs.Legend{Display: types.False}
				link := `<a href="index.html">back to index</a>`
				saveCharts(fmt.Sprintf("%s-roc-%s.html", base, chrom), "", link, c)
				chartjs.XFloatFormat = tmp
				asPng(fmt.Sprintf("%s-roc-%s.png", base, chrom), c, 4, 3)
			}
		}
	}
	for i, s := range slopes {
		slopes[i] = s / float32(nSlopes)
	}
	checkSexes(sexes, cli.sex)
	return sexes, offs, pca8, chromNames, slopes
}
// updateSlopes adjusts the slopes slice for each sample.
// The value is the slope between 1+/-delta scaled by scalar
// where scalar is likely chromosome length to weight chromosomes.
func updateSlopes(rocs [][]float32, scalar float32, slopes []float32) {
	//mid := slotsMid * slots
	n := 0.1
	ilo := int(0.5 + (slotsMid-n)*slots)
	ihi := int(0.5 + (slotsMid+n)*slots)
	// value around 1 is: (0.6666+/-0.15)/0.6666
	for i := range slopes {
		vals := rocs[i]
		lo, hi := vals[ilo], vals[ihi]
		slopes[i] += float32(lo-hi) * scalar
	}
}
func keys(o map[string][]float64) []string {
	skeys := make([]string, 0, len(o))
	for k := range o {
		skeys = append(skeys, k)
	}
	return skeys
}
func checkSexes(obs map[string][]float64, exp []string) {
	if len(obs) != len(exp) {
		msg := fmt.Sprintf("indexcov: expected %d sex chromosomes, found: %d.", len(exp), len(obs))
		msg += fmt.Sprintf("\nyou can set the expected with --sex '%s'", strings.Join(keys(obs), ","))
		// if it found no sex chromosomes *and* it was not the default, then error.
		// but it it was the default, it's just a warning.
		if len(obs) == 0 && !reflect.DeepEqual(exp, []string{"X", "Y"}) {
			log.Fatal("(FATAL) " + msg)
		}
		fmt.Fprintln(os.Stderr, "(WARNING) "+msg)
	}
}
func pca(pca8 [][]uint8, samples []string) (*mat.Dense, []chartjs.Chart, string) {
	imat := mat.NewDense(len(pca8), len(pca8[0]), nil)
	row := make([]float64, len(pca8[0]))
	for i := 0; i < len(pca8); i++ {
		for j, v := range pca8[i] {
			row[j] = float64(v)
		}
		imat.SetRow(i, row)
	}
	var pc stat.PC
	if ok := pc.PrincipalComponents(imat, nil); !ok {
		panic("indexcov: error with principal components")
	}
	k := 5
	vars := pc.VarsTo(nil)
	floats.Scale(1/floats.Sum(vars), vars)
	if len(vars) < k {
		k = len(vars)
		log.Printf("got: %d principal components", len(vars))
		if k < 3 {
			log.Printf("indexcov: %d principal components, not plotting", k)
			return nil, nil, ""
		}
	}
	vars = vars[:k]
	var proj mat.Dense
	var dst mat.Dense
	pc.VectorsTo(&dst)
	proj.Mul(imat, dst.Slice(0, len(pca8[0]), 0, k))
	pcaPlots, customjs := plotPCA(&proj, samples, vars)
	return &proj, pcaPlots, customjs
}
func getBase(directory string) string {
	prefix := filepath.Base(directory)
	return directory + string(os.PathSeparator) + prefix + "-indexcov"
}