msisensor/bamreader.cpp at master · ding-lab/msisensor · GitHub

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* bamreader.cpp for MSIsensor

* This program is free software: you can redistribute it and/or modify

* it under the terms of the GNU General Public License as published by

* the Free Software Foundation, either version 3 of the License, or

* (at your option) any later version.

* This program is distributed in the hope that it will be useful,

* but WITHOUT ANY WARRANTY; without even the implied warranty of

* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

* GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with this program. If not, see <http://www.gnu.org/licenses/>.

// System header files

#include <iomanip>

#include <iostream>

#include <fstream>

#include <cmath>

#include <assert.h>

// Samtools header files

#include "bam.h"

#include "sam.h"

#include "kstring.h"

#include "kseq.h"

#include "khash.h"

#include "ksort.h"

// Bam header files

#include "bamreader.h"

#include "distribution.h"

// Static function declaration

static int fetch_func_SR (const bam1_t * b1, void *data);

unsigned int g_InWinPlus = 0;

unsigned int g_InWinMinus = 0;

unsigned int g_NumReadScanned = 0;

unsigned int g_NumReadInWindow = 0;

unsigned int g_CloseMappedPlus = 0;

unsigned int g_CloseMappedMinus = 0;

//init hash/maps for read pairing on the fly

KSORT_INIT_GENERIC (uint32_t) KHASH_MAP_INIT_STR (read_name, bam1_t *)

struct fetch_func_data_SR {

fetch_func_data_SR () {

LeftReads = NULL;

read_to_map_qual = NULL;

header = NULL;

b1_flags = NULL;

b2_flags = NULL;

Tag = "";

InsertSize = 0;

}

std::vector < SPLIT_READ > *LeftReads;

khash_t (read_name) * read_to_map_qual;

bam_header_t *header;

flags_hit *b1_flags;

flags_hit *b2_flags;

std::string Tag;

int InsertSize;

};

void parse_flags_and_tags (const bam1_t * b, flags_hit * flags) {

const bam1_core_t *c = &b->core;

char xt_code = '\0';

int mf_code = 0, nm_code = 0, best_hits = 0;

flags->unique = 0;

flags->mapped = !(c->flag & BAM_FUNMAP);

uint8_t *s = bam_aux_get (b, "XT");

if (s != 0) {

xt_code = bam_aux2A (s);

if (xt_code == 'U') {

flags->unique = 1;

} else {

flags->unique = 0;

}

} else { flags->unique = 1; }

s = NULL;

s = bam_aux_get (b, "X0");

if (s != 0) {

best_hits = bam_aux2i (s);

}

s = NULL;

s = bam_aux_get (b, "X1");

if (s != 0) {

int sub_hits = bam_aux2i (s);

if (best_hits + sub_hits == 1) {

flags->suboptimal = 0;

} else { flags->suboptimal = 1; }

} else { flags->suboptimal = 0; }

if (xt_code == 'M' || mf_code == 130) {

//short term fix to unset unique if the maq read was s-w mapped.

//bwa can't set U and M at once.

flags->sw = 1;

} else { flags->sw = 0; }

s = NULL;

s = bam_aux_get (b, "NM");

if (s != 0) {

nm_code = bam_aux2i (s);

flags->edits = nm_code;

} else {

nm_code = 0;

flags->edits = nm_code;

}

return;

}

static int fetch_func_ALL (const bam1_t * b1, void *data) {

fetch_func_data_SR *data_for_bam = (fetch_func_data_SR *) data;

khash_t (read_name) * read_to_map_qual = (khash_t (read_name) *) data_for_bam->read_to_map_qual;

flags_hit *b1_flags = data_for_bam->b1_flags;

flags_hit *b2_flags = data_for_bam->b2_flags;

//SPLIT_READ Temp_One_Read;

const bam1_core_t *b1_core;

bam1_t *b2;

bam1_core_t *b2_core;

b1_core = &b1->core;

std::string read_name = bam1_qname (b1);

khint_t key = kh_get (read_name, read_to_map_qual, bam1_qname (b1));

if (key == kh_end (read_to_map_qual)) {

int ret = 0;

key = kh_put (read_name, read_to_map_qual, strdup (bam1_qname (b1)), &ret);

kh_value (read_to_map_qual, key) = bam_dup1 (b1);

return 0;

} else {

b2 = bam_dup1 (kh_value (read_to_map_qual, key));

bam_destroy1 (kh_value (read_to_map_qual, key));

b2_core = &b2->core;

//this seems stupid, but in order to manage the read names, necessary

free ((char *) kh_key (read_to_map_qual, key));

kh_del (read_name, read_to_map_qual, key);

std::string c_sequence;

}

parse_flags_and_tags (b1, b1_flags);

parse_flags_and_tags (b2, b2_flags);

build_record(b1, b2, data, b1_flags);

build_record(b2, b1, data, b2_flags);

bam_destroy1 (b2);

return 0;

}

// new version fetch function for single end_reads

static int fetch_func_ALL (const bam1_t * b1, void *data) {

fetch_func_data_SR *data_for_bam = (fetch_func_data_SR *) data;

khash_t (read_name) * read_to_map_qual = (khash_t (read_name) *) data_for_bam->read_to_map_qual;

flags_hit *b1_flags = data_for_bam->b1_flags;

//SPLIT_READ Temp_One_Read;

const bam1_core_t *b1_core;

b1_core = &b1->core;

parse_flags_and_tags (b1, b1_flags);

build_record( b1, data, b1_flags );

return 0;

}

/** 'ReadInRead' reads in reads from Pindel input file. */

bool ReadInBamReads( const char *bam_path,

const std::string & FragName,

unsigned start,

unsigned end,

std::vector < SPLIT_READ > & AllReads,

std::string Tag) {

bamFile fp;

fp = bam_open (bam_path, "r");

assert (fp);

bam_index_t *idx;

idx = bam_index_load (bam_path); // load BAM index

assert (idx);

bam_header_t *header = bam_header_read (fp);

bam_init_header_hash (header);

assert (header);

int tid;

tid = bam_get_tid (header, FragName.c_str ());

fetch_func_data_SR data;

data.header = header;

data.LeftReads = &AllReads;

data.read_to_map_qual = NULL;

data.read_to_map_qual = kh_init (read_name);

flags_hit b1_flags, b2_flags;

data.b1_flags = &b1_flags;

data.b2_flags = &b2_flags;

data.Tag = Tag;

// std:: cout << " before bam_fetch " << std::endl;

// give warning and abort if using dif refs

if (tid == -1) {

std::cout << "Program aborted: " << std::endl;

std::cout << "Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!"<<std::endl;

exit(1);

}

bam_fetch (fp, idx, tid, start, end, &data, fetch_func_ALL);

// std:: cout << " after bam_fetch " << std::endl;

khint_t key;

if (kh_size (data.read_to_map_qual) > 0) {

for (key = kh_begin (data.read_to_map_qual); key != kh_end (data.read_to_map_qual); ++key) {

if (kh_exist (data.read_to_map_qual, key)) {

bam_destroy1 (kh_value (data.read_to_map_qual, key));

free ((char *) kh_key (data.read_to_map_qual, key));

}

kh_clear (read_name, data.read_to_map_qual);

kh_destroy (read_name, data.read_to_map_qual);

bam_header_destroy (header);

bam_index_destroy (idx);

bam_close (fp);

return true;

}

// new version build_record for single end reads

void build_record( const bam1_t * current_read,

void *data,

const flags_hit *flag_current_read ) {

SPLIT_READ Temp_One_Read;

fetch_func_data_SR *data_for_bam = (fetch_func_data_SR *) data;

bam_header_t *header = (bam_header_t *) data_for_bam->header;

std::string Tag = (std::string) data_for_bam->Tag;

const bam1_core_t *current_core;

current_core = &current_read->core;

// Determine sample name for read.

// std::string c_sequence;

uint8_t *s = bam1_seq (current_read);

for (int i = 0; i <current_core->l_qseq; ++i) {

Temp_One_Read.ReadSeq.append (1, bam_nt16_rev_table[bam1_seqi (s, i)]);

}

//std::cout<<Temp_One_Read.ReadSeq<<"\n";

if ( !flag_current_read->mapped ) {

Temp_One_Read.Mapped = false;

} else {

Temp_One_Read.MatchedRelPos = current_core->pos;

Temp_One_Read.Mapped = true;

}

//std::cout<< Temp_One_Read.MatchedRelPos <<"\n";

// load one read

data_for_bam->LeftReads->push_back(Temp_One_Read);

return;

}

void build_record( const bam1_t * current_read,

const bam1_t * mate_read,

void *data,

const flags_hit *flag_current_read ) {

SPLIT_READ Temp_One_Read;

fetch_func_data_SR *data_for_bam = (fetch_func_data_SR *) data;

bam_header_t *header = (bam_header_t *) data_for_bam->header;

std::string Tag = (std::string) data_for_bam->Tag;

const bam1_core_t *current_core;

const bam1_core_t *mate_core;

current_core = &current_read->core;

mate_core = &mate_read->core;

// Determine sample name for read.

// std::string c_sequence;

uint8_t *s = bam1_seq (current_read);

for (int i = 0; i <current_core->l_qseq; ++i) {

Temp_One_Read.ReadSeq.append (1, bam_nt16_rev_table[bam1_seqi (s, i)]);

}

//std::cout<<Temp_One_Read.ReadSeq<<"\n";

if ( !flag_current_read->mapped ) {

Temp_One_Read.Mapped = false;

} else {

Temp_One_Read.MatchedRelPos = current_core->pos;

Temp_One_Read.Mapped = true;

}

//std::cout<< Temp_One_Read.MatchedRelPos <<"\n";

// load one read

data_for_bam->LeftReads->push_back(Temp_One_Read);

return;

}

int32_t bam_cigar2len (const bam1_core_t * c, const uint32_t * cigar) {

uint32_t k;

int32_t l = 0;

for (k = 0; k < c->n_cigar; ++k) {

int op = cigar[k] & BAM_CIGAR_MASK;

if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP) {

l += cigar[k] >> BAM_CIGAR_SHIFT;

}

if (op == BAM_CDEL) {

l -= cigar[k] >> BAM_CIGAR_SHIFT;

}

return l;

}

int32_t bam_cigar2mismatch( const bam1_core_t *readCore, const uint32_t *cigar) {

uint32_t cigarIndex;

int32_t numberOfMismatches = 0;

for (cigarIndex = 0; cigarIndex < readCore->n_cigar; ++cigarIndex) {

int elementType = cigar[cigarIndex] & BAM_CIGAR_MASK;

if (elementType != BAM_CMATCH) {

numberOfMismatches += cigar[cigarIndex] >> BAM_CIGAR_SHIFT;

}

return numberOfMismatches;

}

msisensor/bamreader.cpp at master · ding-lab/msisensor · GitHub

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