func pasta_filter(pasta_stream *bufio.Reader, out *bufio.Writer, start, n int) error {
var msg pasta.ControlMessage
var pasta_stream_pos int
var dbp int
_ = dbp
var curStreamState int
_ = curStreamState
var pasta_ref_pos int
_ = pasta_ref_pos
ref_pos := 0
message_processed_flag := false
for {
//var ch1 byte
ch, e := pasta_stream.ReadByte()
for (e == nil) && ((ch == '\n') || (ch == ' ') || (ch == '\r') || (ch == '\t')) {
ch, e = pasta_stream.ReadByte()
}
if e != nil {
break
}
if ch == '>' {
msg, e = pasta.ControlMessageProcess(pasta_stream)
if e != nil {
return fmt.Errorf("invalid control message")
}
if (msg.Type == pasta.REF) || (msg.Type == pasta.NOC) {
curStreamState = pasta.MSG
} else if msg.Type == pasta.POS {
ref_pos = msg.RefPos
} else {
//ignore
//
continue
}
pasta.ControlMessagePrint(&msg, out)
message_processed_flag = true
continue
}
if message_processed_flag {
out.WriteByte('\n')
}
message_processed_flag = false
pasta_stream_pos++
// special case: nop
//
if ch == '.' {
continue
}
dbp = pasta.RefDelBP[ch]
//anch_bp := ch
is_del := false
_ = is_del
is_ins := false
_ = is_ins
is_ref := false
_ = is_ref
is_noc := false
_ = is_noc
if ch == '!' || ch == '$' || ch == '7' || ch == 'E' || ch == 'z' {
is_del = true
} else if ch == 'Q' || ch == 'S' || ch == 'W' || ch == 'd' || ch == 'Z' {
is_ins = true
} else if ch == 'a' || ch == 'c' || ch == 'g' || ch == 't' {
is_ref = true
} else if ch == 'n' || ch == 'N' || ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' {
is_noc = true
}
if (ref_pos >= start) && (ref_pos < (start + n)) {
out.WriteByte(ch)
}
// Add to reference sequence
//
for {
if is_ins {
break
}
ref_pos++
break
}
}
return nil
}
func interleave_filter(pasta_stream *bufio.Reader, out *bufio.Writer, start, n int) error {
var msg pasta.ControlMessage
var e error
var e0 error
var pasta_stream0_pos, pasta_stream1_pos int
var dbp0, dbp1 int
_, _ = dbp0, dbp1
var curStreamState int
_ = curStreamState
var pasta_ref_pos int
_ = pasta_ref_pos
bp_count := 0
lfmod := 50
_ = lfmod
ref_pos := 0
ch := [2]byte{}
message_processed_flag := false
for {
//var ch1 byte
var e1 error
ch[0], e0 = pasta_stream.ReadByte()
for (e0 == nil) && ((ch[0] == '\n') || (ch[0] == ' ') || (ch[0] == '\r') || (ch[0] == '\t')) {
ch[0], e0 = pasta_stream.ReadByte()
}
if e0 != nil {
break
}
if ch[0] == '>' {
msg, e = pasta.ControlMessageProcess(pasta_stream)
if e != nil {
return fmt.Errorf("invalid control message")
}
if (msg.Type == pasta.REF) || (msg.Type == pasta.NOC) {
curStreamState = pasta.MSG
} else if msg.Type == pasta.POS {
ref_pos = msg.RefPos
}
pasta.ControlMessagePrint(&msg, out)
message_processed_flag = true
continue
}
if message_processed_flag {
out.WriteByte('\n')
}
message_processed_flag = false
ch[1], e1 = pasta_stream.ReadByte()
for (e1 == nil) && ((ch[1] == '\n') || (ch[1] == ' ') || (ch[1] == '\r') || (ch[1] == '\t')) {
ch[1], e1 = pasta_stream.ReadByte()
}
if e1 != nil {
break
}
pasta_stream0_pos++
pasta_stream1_pos++
// special case: nop
//
if ch[0] == '.' && ch[1] == '.' {
continue
}
dbp0 = pasta.RefDelBP[ch[0]]
dbp1 = pasta.RefDelBP[ch[1]]
anch_bp := ch[0]
if anch_bp == '.' {
anch_bp = ch[1]
}
is_del := []bool{false, false}
is_ins := []bool{false, false}
is_ref := []bool{false, false}
_ = is_ref
is_noc := []bool{false, false}
_ = is_noc
for aa := 0; aa < 2; aa++ {
if ch[aa] == '!' || ch[aa] == '$' || ch[aa] == '7' || ch[aa] == 'E' || ch[aa] == 'z' {
is_del[aa] = true
} else if ch[aa] == 'Q' || ch[aa] == 'S' || ch[aa] == 'W' || ch[aa] == 'd' || ch[aa] == 'Z' {
is_ins[aa] = true
} else if ch[aa] == 'a' || ch[aa] == 'c' || ch[aa] == 'g' || ch[aa] == 't' {
is_ref[aa] = true
} else if ch[aa] == 'n' || ch[aa] == 'N' || ch[aa] == 'A' || ch[aa] == 'C' || ch[aa] == 'G' || ch[aa] == 'T' {
is_noc[aa] = true
}
}
if (is_ins[0] && (!is_ins[1] && ch[1] != '.')) ||
(is_ins[1] && (!is_ins[0] && ch[0] != '.')) {
return fmt.Errorf(fmt.Sprintf("insertion mismatch (ch %c,%c ord(%v,%v) @ %v)", ch[0], ch[1], ch[0], ch[1], bp_count))
}
if (ref_pos >= start) && (ref_pos < (start + n)) {
if ref_pos == start {
out.WriteString(fmt.Sprintf(">P{%d}\n", ref_pos))
}
out.WriteByte(ch[0])
out.WriteByte(ch[1])
}
// Add to reference sequence
//
for {
if is_ins[0] || is_ins[1] {
break
}
ref_pos++
break
}
}
return nil
}
