SYMBOL INDEX (308 symbols across 33 files)

FILE: cmd/goleft/goleft.go
  type progPair (line 19) | type progPair struct
  function printProgs (line 33) | func printProgs(ret int) {
  function main (line 56) | func main() {

FILE: cnveval/cmd/cnveval/cnveval.go
  type cliargs (line 17) | type cliargs struct
  function main (line 24) | func main() {
  function asCNV (line 56) | func asCNV(ts []cnveval.Truth) []cnveval.CNV {
  function parseTruth (line 65) | func parseTruth(p string, cnt bool, samples map[string]bool) []cnveval.T...
  function mustAtoi (line 109) | func mustAtoi(s string) int {
  function parseLine (line 117) | func parseLine(l string) cnveval.Truth {

FILE: cnveval/cnveval.go
  type CNV (line 11) | type CNV struct
    method String (line 34) | func (c CNV) String() string {
  type Truth (line 21) | type Truth struct
    method String (line 30) | func (t Truth) String() string {
    method equals (line 38) | func (t Truth) equals(o Truth) bool {
  type SC (line 43) | type SC
    method Order (line 53) | func (s SC) Order() int {
    method String (line 68) | func (s SC) String() string {
  type TS (line 84) | type TS struct
  type Stat (line 89) | type Stat struct
    method String (line 93) | func (s Stat) String() string {
    method Recall (line 98) | func (s Stat) Recall() float64 {
    method Precision (line 101) | func (s Stat) Precision() float64 {
  type CohortStats (line 105) | type CohortStats
    method TP (line 107) | func (c CohortStats) TP(class SC) int {
    method Tabulate (line 118) | func (c CohortStats) Tabulate() [4]Stat {
    method Precision (line 135) | func (c CohortStats) Precision(class SC) float64 {
    method Recall (line 148) | func (c CohortStats) Recall(class SC) float64 {
  function Evaluate (line 163) | func Evaluate(cnvs []CNV, truths []Truth, po float64) CohortStats {
  function notin (line 214) | func notin(a string, bs []string) bool {
  function fromMap (line 223) | func fromMap(samples map[string]bool) []string {
  function updateFP (line 231) | func updateFP(stat map[TS]*Stat, others []Truth, cnvs []CNV, truths []Tr...
  function updatePositive (line 289) | func updatePositive(stat map[TS]*Stat, truths []Truth, cnvs []CNV, po fl...
  function sizeClass (line 343) | func sizeClass(t Truth) SC {
  function sameCN (line 354) | func sameCN(a, b int) bool {
  function imin (line 364) | func imin(a, b int) int {
  function imax (line 371) | func imax(a, b int) int {
  function poverlap (line 378) | func poverlap(a CNV, b Truth) float64 {

FILE: covstats/covstats.go
  function pcheck (line 28) | func pcheck(e error) {
  constant N_MADS (line 34) | N_MADS = 10
  function readCoverage (line 36) | func readCoverage(path string) int {
  function madFilter (line 57) | func madFilter(arr []int, nmads int) []int {
  function meanStd (line 78) | func meanStd(arr []int) (mean, std float64) {
  type Stats (line 92) | type Stats struct
    method String (line 114) | func (s Stats) String() string {
  constant skipReads (line 119) | skipReads = 100000
  function BamStats (line 122) | func BamStats(br *bam.Reader, n int, skipReads int) Stats {
  function Main (line 223) | func Main() {

FILE: dcnv/dcnv.go
  type Intervals (line 25) | type Intervals struct
    method NSamples (line 45) | func (ivs Intervals) NSamples() int {
    method addFromLine (line 78) | func (ivs *Intervals) addFromLine(l string, fa *faidx.Faidx, fp *faidx...
    method SampleMedians (line 108) | func (ivs *Intervals) SampleMedians() []float64 {
    method NormalizeBySampleMedian (line 128) | func (ivs *Intervals) NormalizeBySampleMedian() {
    method ReadRegions (line 153) | func (ivs *Intervals) ReadRegions(path string, fasta string) {
    method Write (line 188) | func (ivs *Intervals) Write(n int) {
  function mustAtoi (line 50) | func mustAtoi(a string) uint32 {
  function mustAtof (line 58) | func mustAtof(a string) float64 {
  function imin (line 66) | func imin(a, b int) int {
  type GcBounds (line 73) | type GcBounds struct
  function median (line 138) | func median(b []float64) float64 {
  type MatFn (line 151) | type MatFn
  function Pipeliner (line 210) | func Pipeliner(mat *mat.Dense, fns ...MatFn) {
  constant cnMax (line 217) | cnMax = 2.5
  type vs (line 219) | type vs struct
    method Xs (line 224) | func (v *vs) Xs() []float64 {
    method Ys (line 228) | func (v *vs) Ys() []float64 {
    method Rs (line 232) | func (v *vs) Rs() []float64 {
    method Len (line 236) | func (v *vs) Len() int {
    method XY (line 242) | func (v *vs) XY(i int) (x, y float64) {
  function asValues (line 246) | func asValues(vals []float64, multiplier float64) chartjs.Values {
  function randomColor (line 265) | func randomColor(s int) *types.RGBA {
  function plotDepths (line 274) | func plotDepths(depths *mat.Dense, samples []string, chrom string, base ...
  function main (line 323) | func main() {

FILE: dcnv/debiaser/debiaser.go
  type Debiaser (line 16) | type Debiaser interface
  type Sorter (line 21) | type Sorter interface
  type SortedDebiaser (line 28) | type SortedDebiaser interface
  type GeneralDebiaser (line 37) | type GeneralDebiaser struct
    method setTmp (line 44) | func (g *GeneralDebiaser) setTmp(r, c int) {
    method Sort (line 56) | func (g *GeneralDebiaser) Sort(mat *mat.Dense) {
    method Unsort (line 79) | func (g *GeneralDebiaser) Unsort(mat *mat.Dense) {
    method Debias (line 98) | func (g *GeneralDebiaser) Debias(imat *mat.Dense) {
  type ChunkDebiaser (line 125) | type ChunkDebiaser struct
    method Debias (line 133) | func (cd *ChunkDebiaser) Debias(imat *mat.Dense) {
  type SVD (line 173) | type SVD struct
    method Debias (line 177) | func (isvd *SVD) Debias(imat *mat.Dense) {
  function extractSVD (line 202) | func extractSVD(svd *mat.SVD) (s []float64, u, v *mat.Dense) {

FILE: dcnv/debiaser/debiaser_test.go
  function fillMatrix (line 15) | func fillMatrix(mat *mat.Dense) {
  function printMatrix (line 24) | func printMatrix(imat *mat.Dense) {
  function TestGeneralDebiasSort (line 40) | func TestGeneralDebiasSort(t *testing.T) {
  function TestGeneralDebias (line 89) | func TestGeneralDebias(t *testing.T) {

FILE: dcnv/scalers/scalers.go
  type Scaler (line 15) | type Scaler interface
  type ZScore (line 25) | type ZScore struct
    method UnScale (line 31) | func (z *ZScore) UnScale(a *mat.Dense) {
    method Scale (line 42) | func (z *ZScore) Scale(a *mat.Dense) {
  type RowCentered (line 58) | type RowCentered struct
    method Scale (line 68) | func (rc *RowCentered) Scale(a *mat.Dense) {
    method UnScale (line 102) | func (rc *RowCentered) UnScale(a *mat.Dense) {
  type ColCentered (line 63) | type ColCentered struct
    method Scale (line 84) | func (cc *ColCentered) Scale(a *mat.Dense) {
    method UnScale (line 113) | func (cc *ColCentered) UnScale(a *mat.Dense) {
  function gmean (line 126) | func gmean(vs []float64) float64 {
  type Log2 (line 135) | type Log2 struct
    method Scale (line 140) | func (l *Log2) Scale(a *mat.Dense) {
    method UnScale (line 155) | func (l *Log2) UnScale(a *mat.Dense) {

FILE: dcnv/scalers/scalers_test.go
  constant eps (line 15) | eps = 0.001
  function TestZScoreRoundTrip (line 17) | func TestZScoreRoundTrip(t *testing.T) {
  function TestLog2RoundTrip (line 49) | func TestLog2RoundTrip(t *testing.T) {

FILE: depth/depth.go
  type dargs (line 27) | type dargs struct
  constant command (line 45) | command = "echo '%s'; samtools depth -Q %d -d %d -r '%s' '%s'"
  function pcheck (line 52) | func pcheck(e error) {
  function min (line 58) | func min(a, b int) int {
  function max (line 65) | func max(a, b int) int {
  function chromStartEndFromLine (line 75) | func chromStartEndFromLine(line []byte) (string, int, int) {
  function regionFromLine (line 96) | func regionFromLine(line []byte) string {
  function genFromBed (line 103) | func genFromBed(ch chan string, args dargs) {
  function genCommands (line 122) | func genCommands(args dargs) chan string {
  function Main (line 162) | func Main() {
  type ipos (line 177) | type ipos struct
  function mean (line 181) | func mean(sl []int, l int) (avg float64) {
  function getStats (line 191) | func getStats(fa *faidx.Faidx, chrom string, start, end int) string {
  function getPosDepth (line 202) | func getPosDepth(rline string) (int, int, error) {
  function getCovClass (line 223) | func getCovClass(depth, minCov, maxMeanDepth int) string {
  function run (line 236) | func run(args dargs) {

FILE: depth/intervals.go
  type irange (line 12) | type irange struct
    method Overlap (line 17) | func (i irange) Overlap(b interval.IntRange) bool {
    method ID (line 21) | func (i irange) ID() uintptr              { return i.UID }
    method Range (line 22) | func (i irange) Range() interval.IntRange { return interval.IntRange{i...
  function Overlaps (line 25) | func Overlaps(tree *interval.IntTree, start, end int) bool {
  function ReadTree (line 42) | func ReadTree(ps ...string) map[string]*interval.IntTree {

FILE: depthwed/depthwed.go
  type cliargs (line 18) | type cliargs struct
  function pcheck (line 23) | func pcheck(e error) {
  function Main (line 30) | func Main() {
  function getNameFromFile (line 37) | func getNameFromFile(f string) string {
  function run (line 48) | func run(args cliargs) {
  type depth (line 75) | type depth struct
  function mustAtoi (line 82) | func mustAtoi(s string) int {
  function mustAtof (line 87) | func mustAtof(s string) float64 {
  function sFromLine (line 93) | func sFromLine(l string) depth {
  function getNextChrom (line 108) | func getNextChrom(r *bufio.Reader) string {
  function next (line 117) | func next(beds []*xopen.Reader, size int) (depths []depth, eof bool) {

FILE: emdepth/emdepth.go
  function median32 (line 18) | func median32(a []float32) float64 {
  function mean32 (line 32) | func mean32(a []float32) float32 {
  function mean64 (line 40) | func mean64(a []float64) float64 {
  function abs (line 51) | func abs(a float64) float64 {
  function abs32 (line 58) | func abs32(a float32) float32 {
  constant maxCN (line 65) | maxCN = 8
  constant maxiter (line 66) | maxiter = 10
  constant eps (line 67) | eps = 0.01
  function summaxdiff (line 71) | func summaxdiff(a, b []float64) (float64, float64) {
  function getBins (line 83) | func getBins(nSamples int) [][]float64 {
  function init (line 97) | func init() {
  type Position (line 103) | type Position struct
    method String (line 108) | func (p *Position) String() string {
  function EMDepth (line 117) | func EMDepth(depths []float32, p Position) *EMD {
  type EMD (line 209) | type EMD struct
    method Same (line 227) | func (e *EMD) Same(o *EMD) (non2 []int, changed []int, pct float64) {
    method Log2FC (line 250) | func (e *EMD) Log2FC() []float64 {
    method CN (line 263) | func (e *EMD) CN() []int {
    method Type (line 272) | func (e *EMD) Type(d float32) int {
    method adjustCN (line 293) | func (e *EMD) adjustCN(cn int, depth float64) int {
  constant lower (line 224) | lower = -0.80
  constant upper (line 225) | upper = 0.40
  type Cache (line 310) | type Cache struct
    method Add (line 330) | func (c *Cache) Add(e *EMD) []*CNV {
    method Clear (line 348) | func (c *Cache) Clear(p *Position) []*CNV {
  type CNV (line 317) | type CNV struct
    method String (line 326) | func (c *CNV) String() string {
  function makecnvs (line 376) | func makecnvs(es []*EMD, sampleI int) *CNV {

FILE: emdepth/emdepth_test.go
  function TestDepth (line 11) | func TestDepth(t *testing.T) {
  function TestBig (line 28) | func TestBig(t *testing.T) {
  function BenchmarkEMDepth (line 56) | func BenchmarkEMDepth(b *testing.B) {

FILE: emdepth/mops/mops.go
  function mean32 (line 7) | func mean32(a []float32) float32 {
  function abs (line 15) | func abs(a float64) float64 {
  function abs32 (line 22) | func abs32(a float32) float32 {
  constant maxCN (line 29) | maxCN = 8
  constant delta (line 30) | delta = 0.001
  constant maxiter (line 31) | maxiter = 10
  constant eps (line 33) | eps = 0.001
  function pmf (line 35) | func pmf(k int, pmean float64) float64 {
  function pdepth (line 41) | func pdepth(depths []float32, cn int, lambda float32, out []float32) {
  function estep (line 54) | func estep(alpha []float32, depths []float32, lambda float32, aik [][]fl...
  function mstep (line 90) | func mstep(depths []float32, adepths [][]float32) (alpha []float32, lamb...
  type Mopped (line 121) | type Mopped struct
    method Gain (line 126) | func (m *Mopped) Gain() float32 {
  function Mops (line 139) | func Mops(depths []float32) *Mopped {
  function CNINI (line 163) | func CNINI(cns []int, depths []float32, centers []float64) float32 {

FILE: emdepth/mops/mops_test.go
  function TestDepth (line 10) | func TestDepth(t *testing.T) {
  function TestBig (line 27) | func TestBig(t *testing.T) {
  function TestMops (line 37) | func TestMops(t *testing.T) {

FILE: emdepth/stats.go
  function init (line 7) | func init() {
  function pmf (line 14) | func pmf(k int, mu float64) float64 {
  function cdf (line 25) | func cdf(mu float64, k int) float64 {

FILE: goleft.go
  constant Version (line 3) | Version = "0.2.6"

FILE: indexcov/anonymize/main.go
  function main (line 16) | func main() {

FILE: indexcov/crai/crai.go
  type Slice (line 17) | type Slice struct
    method Start (line 27) | func (s Slice) Start() int64 {
    method SliceBytes (line 31) | func (s Slice) SliceBytes() int32 {
    method Span (line 35) | func (s Slice) Span() int64 {
  type Index (line 39) | type Index struct
    method Sizes (line 45) | func (idx *Index) Sizes() [][]int64 {
    method makeSizes (line 56) | func (idx *Index) makeSizes(slices []Slice) []int64 {
  constant TileWidth (line 43) | TileWidth = 16384
  function ReadIndex (line 129) | func ReadIndex(r io.Reader) (*Index, error) {

FILE: indexcov/crai/crai_test.go
  function TestCrai (line 11) | func TestCrai(t *testing.T) {
  function TestSizes (line 1040) | func TestSizes(t *testing.T) {

FILE: indexcov/crai/plot-vs-with-st-depth.py
  function read (line 6) | def read(path):

FILE: indexcov/crai/st-depth-to-bins.py
  function gen (line 6) | def gen():

FILE: indexcov/indexcov.go
  type Index (line 57) | type Index struct
    method Path (line 69) | func (i *Index) Path() string {
    method Sizes (line 74) | func (i *Index) Sizes() [][]int64 {
    method init (line 83) | func (x *Index) init() {
    method NormalizedDepth (line 129) | func (x *Index) NormalizedDepth(refID int) []float32 {
  function vOffset (line 78) | func vOffset(o bgzf.Offset) int64 {
  constant slots (line 153) | slots = 70
  constant slotsMid (line 157) | slotsMid = float64(2) / float64(3)
  function tint (line 159) | func tint(f float32) int {
  function CountsAtDepth (line 170) | func CountsAtDepth(depths []float32, counts []int) {
  function CountsROC (line 181) | func CountsROC(counts []int) []float32 {
  function getRef (line 195) | func getRef(b *bam.Reader, chrom string) *sam.Reference {
  function GetShortName (line 213) | func GetShortName(b string, isCrai bool) (string, error) {
  function getWriter (line 248) | func getWriter(base string) (*bgzf.Writer, error) {
  function zero (line 259) | func zero(ints []int) {
  function getDirectory (line 265) | func getDirectory(path string) (bool, error) {
  function ReadFai (line 278) | func ReadFai(path string, chrom string) []*sam.Reference {
  function RefsFromBam (line 320) | func RefsFromBam(path string, chrom string) []*sam.Reference {
  function getReferences (line 344) | func getReferences() []*sam.Reference {
  function expandGlobs (line 376) | func expandGlobs(paths []string) []string {
  function Main (line 392) | func Main() {
  type rdi (line 458) | type rdi struct
  function ReadIndex (line 464) | func ReadIndex(path string) *Index {
  function readIndex (line 471) | func readIndex(r rdi) (*Index, string, int) {
  constant maxSamples (line 528) | maxSamples = 100
  function sameChrom (line 530) | func sameChrom(as []string, b string) bool {
  function normalizeAcrossSamples (line 549) | func normalizeAcrossSamples(depths [][]float32) {
  function run (line 599) | func run(refs []*sam.Reference, idxs []*Index, names []string, base stri...
  function updateSlopes (line 739) | func updateSlopes(rocs [][]float32, scalar float32, slopes []float32) {
  function keys (line 752) | func keys(o map[string][]float64) []string {
  function checkSexes (line 760) | func checkSexes(obs map[string][]float64, exp []string) {
  function pca (line 773) | func pca(pca8 [][]uint8, samples []string) (*mat.Dense, []chartjs.Chart,...
  function getBase (line 809) | func getBase(directory string) string {
  function writeIndex (line 815) | func writeIndex(sexes map[string][]float64, counts []*counter, samples [...
  function GetCN (line 957) | func GetCN(depths [][]float32) []float64 {
  function saveCharts (line 993) | func saveCharts(path string, customjs string, customHTML string, charts ...
  function getROCs (line 1008) | func getROCs(counts [][]int) [][]float32 {
  function writeROCs (line 1018) | func writeROCs(counts [][]int, names []string, chrom string, fh io.Write...
  function depthsFor (line 1038) | func depthsFor(depths [][]float32, i int) string {
  type counter (line 1050) | type counter struct
    method count (line 1062) | func (c *counter) count(depths []float32, n int) {

FILE: indexcov/indexcov_test.go
  function TestShortName (line 7) | func TestShortName(t *testing.T) {

FILE: indexcov/paper/cmp.py
  function gen (line 15) | def gen(fh):

FILE: indexcov/paper/scripts/cmp.py
  function gen (line 13) | def gen(fh):

FILE: indexcov/plot.go
  type vs (line 24) | type vs struct
    method Xs (line 29) | func (v *vs) Xs() []float64 {
    method Ys (line 33) | func (v *vs) Ys() []float64 {
    method Rs (line 37) | func (v *vs) Rs() []float64 {
    method Len (line 41) | func (v *vs) Len() int {
    method XY (line 47) | func (v *vs) XY(i int) (x, y float64) {
    method Sample (line 51) | func (v *vs) Sample(nth int) *vs {
  constant cnMax (line 64) | cnMax = 2.5
  function asValues (line 66) | func asValues(vals []float32, multiplier float64) chartjs.Values {
  function init (line 89) | func init() {
  function randomColor (line 98) | func randomColor(s int, check bool) *types.RGBA {
  function plotDepths (line 110) | func plotDepths(depths [][]float32, samples []string, chrom string, base...
  function plotBins (line 166) | func plotBins(counts []*counter, samples []string) (chartjs.Chart, strin...
  function plotBinsSet (line 240) | func plotBinsSet(chart *chartjs.Chart, xys *vs, c *types.RGBA, xa string...
  function plotPCA (line 251) | func plotPCA(imat *mat.Dense, samples []string, vars []float64) ([]chart...
  function plotROCs (line 318) | func plotROCs(rocs [][]float32, samples []string, chrom string) (chartjs...
  function plotMapped (line 355) | func plotMapped(mapped []uint64, unmapped []uint64, samples []string) (*...
  function plotSex (line 412) | func plotSex(sexes map[string][]float64, chroms []string, samples []stri...
  function asPng (line 476) | func asPng(path string, chart chartjs.Chart, wInches float64, hInches fl...
  type ydticks (line 539) | type ydticks struct
    method Ticks (line 542) | func (ydticks) Ticks(min, max float64) []plot.Tick {
  type xdticks (line 540) | type xdticks struct
    method Ticks (line 551) | func (xdticks) Ticks(min, max float64) []plot.Tick {
  function makeMillions (line 564) | func makeMillions(v float64) string {

FILE: indexcov/template.go
  constant chartTemplate (line 3) | chartTemplate = `<!DOCTYPE html>

FILE: indexcov/types.go
  constant TileWidth (line 15) | TileWidth = 0x4000
  constant StatsDummyBin (line 19) | StatsDummyBin = 0x924a
  type oRefIndex (line 22) | type oRefIndex struct
  type bin (line 28) | type bin struct
  type referenceStats (line 33) | type referenceStats struct
  function getSizes (line 45) | func getSizes(idx *bam.Index) ([][]int64, uint64, uint64) {

FILE: indexsplit/indexsplit.go
  type cliargs (line 24) | type cliargs struct
  function imin (line 31) | func imin(a, b int) int {
  function chop (line 38) | func chop(sizes [][]float64) {
  function getPercents (line 52) | func getPercents(sizes [][]float64) ([]float64, []float64) {
  type Chunk (line 69) | type Chunk struct
    method String (line 77) | func (c Chunk) String() string {
  function Split (line 82) | func Split(paths []string, refs []*sam.Reference, N int, probs map[strin...
  function Main (line 197) | func Main() {

FILE: multidepth/multidepth.go
  type dargs (line 18) | type dargs struct
  function chromSize (line 32) | func chromSize(path string, chrom string) int {
  function main (line 49) | func main() {
  function writeOut (line 95) | func writeOut(ch chan []block) *sync.WaitGroup {
  type region (line 116) | type region struct
    method String (line 122) | func (r region) String() string {
  function genRegions (line 126) | func genRegions(l int, chrom string) chan region {
  type site (line 139) | type site struct
  function parseLine (line 144) | func parseLine(line string) site {
  function sufficientDepth (line 163) | func sufficientDepth(s site, a *dargs) bool {
  type block (line 173) | type block struct
    method String (line 180) | func (b block) String() string {
  function splitBlocks (line 184) | func splitBlocks(chrom string, cache []site, a *dargs) []block {
  function aggregate (line 201) | func aggregate(a *dargs, r region, out chan []block) {
  function means (line 270) | func means(sites []site) []string {

FILE: samplename/samplename.go
  function Names (line 14) | func Names(h *sam.Header) []string {
  type cliargs (line 39) | type cliargs struct
    method Version (line 44) | func (c cliargs) Version() string {
  function Main (line 48) | func Main() {