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package vcfgo
import (
"fmt"
"strings"
)
// VCFError satisfies the error interface and allows multiple errors.
// This is useful because, for example, on a single line, every sample may have
// a field that doesn't match the description in the header. We want to keep parsing
// but also let the caller know about the error.
type VCFError struct {
Msgs []string
Lines []int64
}
// Error returns a string with all errors delimited by newlines.
func (e *VCFError) Error() string {
var msgs []string
seen := make(map[string]struct{})
for i, m := range e.Msgs {
// remove duplicates
if _, ok := seen[m]; !ok {
seen[m] = struct{}{}
msgs = append(msgs, fmt.Sprintf("%s. [line: %d]", m, e.Lines[i]))
}
}
return strings.Join(msgs, "\n")
}
// NewVCFError allocates the needed ingredients.
func NewVCFError() *VCFError {
e := VCFError{Msgs: make([]string, 0), Lines: make([]int64, 0)}
return &e
}
// Add adds an error and the line number within the vcf where the error took place.
func (e *VCFError) Add(err error, line int64) {
if err != nil {
if ierr := err.Error(); ierr != "" {
if len(e.Msgs) == 5000 {
// only keep at most 5K errors.
m := make([]string, 0, 5000)
l := make([]int64, 0, 5000)
m = append(m, e.Msgs[3000:]...)
l = append(l, e.Lines[3000:]...)
e.Msgs = m
e.Lines = l
}
e.Msgs = append(e.Msgs, ierr)
e.Lines = append(e.Lines, line)
}
}
}
// IsEmpty returns true if there no errors stored.
func (e *VCFError) IsEmpty() bool {
return len(e.Msgs) == 0
}
// Clear empties the Messages
func (e *VCFError) Clear() {
e.Msgs = e.Msgs[:0]
e.Lines = e.Lines[:0]
}
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