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package shared
import (
"fmt"
"io/ioutil"
"log"
"strings"
. "github.com/brentp/vcfanno/api"
"github.com/shenwei356/xopen"
)
type Config struct {
Annotation []Annotation
PostAnnotation []PostAnnotation
// base path to prepend to all files.
Base string
}
// Annotation holds information about the annotation files parsed from the toml config.
type Annotation struct {
File string
Ops []string
Fields []string
Columns []int
// the names in the output.
Names []string
}
// Flatten turns an annotation into a slice of Sources. Pass in the index of the file.
// having it as a Source makes the code cleaner, but it's simpler for the user to
// specify multiple ops per file in the toml config.
func (a *Annotation) Flatten(index int, basepath string) ([]*Source, error) {
if len(a.Ops) == 0 {
if !strings.HasSuffix(a.File, ".bam") {
return nil, fmt.Errorf("no ops specified for %s\n", a.File)
}
// auto-fill bam to count.
a.Ops = make([]string, len(a.Names))
for i := range a.Names {
a.Ops[i] = "sum"
}
}
if len(a.Columns) == 0 && len(a.Fields) == 0 {
if !strings.HasSuffix(a.File, ".bam") {
return nil, fmt.Errorf("no columns or fields specified for %s\n", a.File)
}
if len(a.Fields) == 0 {
a.Columns = make([]int, len(a.Names))
for i := range a.Names {
a.Columns[i] = 1
}
}
}
if !(xopen.Exists(a.File) || a.File == "-") {
if basepath != "" {
a.File = basepath + "/" + a.File
}
if !(xopen.Exists(a.File) || a.File == "-") {
return nil, fmt.Errorf("[Flatten] unable to open file: %s in %s\n", a.File, basepath)
}
}
n := len(a.Ops)
sources := make([]*Source, n)
for i := 0; i < n; i++ {
isLua := strings.HasPrefix(a.Ops[i], "lua:")
if !isLua {
if len(a.Fields) > i && a.Fields[i] == "DP2" {
if !strings.HasSuffix(a.File, ".bam") {
log.Fatal("DP2 only valid for bams")
}
// always set Op to DP2 whne Field is DP2
a.Ops[i] = "DP2"
}
if _, ok := Reducers[a.Ops[i]]; !ok {
return nil, fmt.Errorf("requested op not found: %s for %s\n", a.Ops[i], a.File)
}
}
op := a.Ops[i]
if len(a.Names) == 0 {
a.Names = a.Fields
}
sources[i] = &Source{File: a.File, Op: op, Name: a.Names[i], Index: index}
if nil != a.Fields {
sources[i].Field = a.Fields[i]
sources[i].Column = -1
} else {
sources[i].Column = a.Columns[i]
}
}
return sources, nil
}
func (c Config) Sources() ([]*Source, error) {
annos := c.Annotation
for i, a := range annos {
if !xopen.Exists(a.File) && a.File != "-" {
a.File = c.Base + "/" + a.File
annos[i] = a
}
}
var s []*Source
for i, a := range annos {
flats, err := a.Flatten(i, c.Base)
if err != nil {
return nil, err
}
s = append(s, flats...)
}
return s, nil
}
func CheckPostAnno(p *PostAnnotation) error {
if len(p.Fields) == 0 {
log.Println("warning: no specified 'fields' for postannotation:", p.Name)
}
if p.Op == "" {
return fmt.Errorf("must specify an 'op' for postannotation")
}
if p.Name == "" {
if p.Op != "delete" {
return fmt.Errorf("must specify a 'name' for postannotation")
}
}
if !(p.Type == "Float" || p.Type == "String" || p.Type == "Integer" || p.Type == "Flag") {
if p.Op != "delete" {
return fmt.Errorf("must specify a type for postannotation that is 'Flag', 'Float', 'Integer' or 'String'")
}
}
return nil
}
func CheckAnno(a *Annotation) error {
if strings.HasSuffix(a.File, ".bam") {
if nil == a.Columns && nil == a.Fields {
a.Columns = []int{1}
}
if nil == a.Ops {
a.Ops = []string{"count"}
}
}
if a.Fields == nil {
// Columns: BED/BAM
if a.Columns == nil {
return fmt.Errorf("must specify either 'fields' or 'columns' for %s", a.File)
}
if len(a.Ops) != len(a.Columns) && !strings.HasSuffix(a.File, ".bam") {
return fmt.Errorf("must specify same # of 'columns' as 'ops' for %s", a.File)
}
if len(a.Names) != len(a.Columns) && !strings.HasSuffix(a.File, ".bam") {
return fmt.Errorf("must specify same # of 'names' as 'ops' for %s", a.File)
}
} else {
// Fields: VCF
if a.Columns != nil {
if strings.HasSuffix(a.File, ".bam") {
a.Columns = make([]int, len(a.Ops))
} else {
return fmt.Errorf("specify only 'fields' or 'columns' not both %s", a.File)
}
}
if len(a.Ops) != len(a.Fields) {
return fmt.Errorf("must specify same # of 'fields' as 'ops' for %s", a.File)
}
}
if len(a.Names) == 0 {
a.Names = a.Fields
}
return nil
}
func ReadLua(lua string) string {
var luaString string
if lua != "" {
luaReader, err := xopen.Ropen(lua)
if err != nil {
log.Fatal(err)
}
luaBytes, err := ioutil.ReadAll(luaReader)
if err != nil {
log.Fatal(err)
}
luaString = string(luaBytes)
} else {
luaString = ""
}
return luaString
}
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