/*
* This attempts to align "seq", which is a string of ACGTacgt letters. It returns
* an array of EasyAlignment objects.
* TODO: Actually return that list.
*/
func GoBwaAlign(ref *GoBwaReference, settings *GoBwaSettings, seq string, arena *Arena) []EasyAlignment {
converted_seq := SequenceConvert(seq)
typed_ref := (*C.bwaidx_t)(ref.BWTData)
//results := C.mem_chain((*C.mem_opt_t)(settings.Settings), typed_ref.bwt, typed_ref.bns, len(converted_seq), &(converted_seq[0]), unsafe.Pointer(uintptr(0)));
results := C.mem_align1_core((*C.mem_opt_t)(settings.Settings),
typed_ref.bwt,
typed_ref.bns,
typed_ref.pac,
(C.int)(len(converted_seq)),
(*C.char)(unsafe.Pointer((&(converted_seq[0])))),
unsafe.Pointer(uintptr(0)))
//algns := make([]*C.mem_alnreg_t, (int)(results.n))
algns := make([]EasyAlignment, (int)(results.n))
arena.Push(uintptr(unsafe.Pointer(results.a)))
for i := (uintptr(0)); i < (uintptr)(results.n); i++ {
a := ((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(results.a)) + i*(unsafe.Sizeof(*results.a)))))
//arena.Push(uintptr(unsafe.Pointer(a)));
p := InterpretAlign(ref, a)
algns[i] = p
//log.Printf("%v", p)
//log.Printf("%v", *((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(results.a)) + i*(unsafe.Sizeof(*results.a))))))
}
return algns
//log.Printf("%v", results);
}
func GoBwaMemMateSW(ref *GoBwaReference, settings *GoBwaSettings, read1 *[]byte, read2 *[]byte, arena *Arena, score_delta int) ([]EasyAlignment, []EasyAlignment) {
typed_ref := (*C.bwaidx_t)(ref.BWTData)
var Pes [4]C.mem_pestat_t
Pes[0].failed = 1
Pes[1].low = -35
Pes[1].high = 500
Pes[1].failed = 0
Pes[1].avg = 200.0
Pes[1].std = 100.0
Pes[2].failed = 1
Pes[3].failed = 1
converted_seq_read1 := SequenceConvert(string(*read1))
converted_seq_read2 := SequenceConvert(string(*read2))
// get mapping for each read
read1_results := C.mem_align1_core((*C.mem_opt_t)(settings.Settings),
typed_ref.bwt,
typed_ref.bns,
typed_ref.pac,
(C.int)(len(converted_seq_read1)),
(*C.char)(unsafe.Pointer((&(converted_seq_read1[0])))),
unsafe.Pointer(uintptr(0)))
read2_results := C.mem_align1_core((*C.mem_opt_t)(settings.Settings),
typed_ref.bwt,
typed_ref.bns,
typed_ref.pac,
(C.int)(len(converted_seq_read2)),
(*C.char)(unsafe.Pointer((&(converted_seq_read2[0])))),
unsafe.Pointer(uintptr(0)))
algns_read1 := make([]EasyAlignment, (int)(read1_results.n))
algns_read2 := make([]EasyAlignment, (int)(read2_results.n))
best_read1_score := 0
best_read2_score := 0
//get some interpretation of these alignments and note the best score for each
for i := (uintptr(0)); i < (uintptr)(read1_results.n); i++ {
a := ((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(read1_results.a)) + i*(unsafe.Sizeof(*read1_results.a)))))
p := InterpretAlign(ref, a)
algns_read1[i] = p
if p.Score > best_read1_score {
best_read1_score = p.Score
}
}
for i := (uintptr(0)); i < (uintptr)(read2_results.n); i++ {
a := ((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(read2_results.a)) + i*(unsafe.Sizeof(*read2_results.a)))))
p := InterpretAlign(ref, a)
algns_read2[i] = p
if p.Score > best_read2_score {
best_read2_score = p.Score
}
}
//rescue alignments for read1 by looping through read2's hits and doing mem_matesw
num := 0
for i := 0; i < len(algns_read2) && num < 50; i++ {
if algns_read2[i].Score >= best_read2_score-score_delta {
// attempt to rescue the read1 alignment here
num++
C.mem_matesw((*C.mem_opt_t)(settings.Settings),
typed_ref.bns,
typed_ref.pac,
&Pes[0],
algns_read2[i].ChainedHit,
(C.int)(len(*read1)),
(*C.uint8_t)(&(converted_seq_read1[0])),
&read1_results)
}
}
algns_read1 = make([]EasyAlignment, (int)(read1_results.n))
for i := (uintptr(0)); i < (uintptr)(read1_results.n); i++ {
a := ((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(read1_results.a)) + i*(unsafe.Sizeof(*read1_results.a)))))
p := InterpretAlign(ref, a)
algns_read1[i] = p
}
//rescue alignments for read2 by looping through read1's hits and doing mem_matesw
num = 0
for i := 0; i < len(algns_read1) && num < 50; i++ {
if algns_read1[i].Score >= best_read1_score-score_delta {
// attempt to rescue the read2 alignment here
num++
C.mem_matesw((*C.mem_opt_t)(settings.Settings),
typed_ref.bns,
typed_ref.pac,
&Pes[0],
algns_read1[i].ChainedHit,
(C.int)(len(*read2)),
(*C.uint8_t)(&(converted_seq_read2[0])),
&read2_results)
}
}
arena.Push(uintptr(unsafe.Pointer(read1_results.a)))
arena.Push(uintptr(unsafe.Pointer(read2_results.a)))
algns_read2 = make([]EasyAlignment, (int)(read2_results.n))
for i := (uintptr(0)); i < (uintptr)(read2_results.n); i++ {
a := ((*C.mem_alnreg_t)(unsafe.Pointer(uintptr(unsafe.Pointer(read2_results.a)) + i*(unsafe.Sizeof(*read2_results.a)))))
p := InterpretAlign(ref, a)
algns_read2[i] = p
}
return algns_read1, algns_read2
}