bam_import.c

#include <zlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <assert.h>
#ifdef _WIN32
#include <fcntl.h>
#endif
#include "tables.h"
#include "kstring.h"
#include "bam.h"
#include "sam_header.h"
#include "kseq.h"
#include "khash.h"

#ifdef _MSC_VER
#define atoll(x) _atoi64(x)
#endif

typedef char *str_p;

KHASH_MAP_INIT_STR(s, int)
KHASH_MAP_INIT_STR(r2l, str_p)
KSTREAM_INIT(gzFile, gzread, 16384)
KHASH_MAP_INIT_STR(ref, uint64_t)

void bam_init_header_hash2(bam_header_t *header);
extern void bam_destroy_header_hash(bam_header_t *header);
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);

unsigned short bam_char2flag_table[256] =
{
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
    BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
    0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
};

struct __tamFile_t
{
    gzFile fp;
    kstream_t *ks;
    kstring_t *str;
    uint64_t n_lines;
    int is_first;
};

char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
{
    char **list = NULL;
    char *s = NULL;
    int n = 0;
    int dret;
    int m = 0;
    gzFile fp = (strcmp(fn, "-") == 0) ? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
    kstream_t *ks;
    kstring_t *str;
    str = (kstring_t*)calloc(1, sizeof(kstring_t));
    ks = ks_init(fp);
    while (ks_getuntil(ks, '\n', str, &dret) > 0)
    {
        if (n == m)
        {
            m = m ? m << 1 : 16;
            list = (char**)realloc(list, m*sizeof(char*));
        }
        if (str->s[str->l-1] == '\r')
            str->s[--str->l] = '\0';
        s = list[n++] = (char*)calloc(str->l + 1, 1);
        strcpy(s, str->s);
    }
    ks_destroy(ks);
    gzclose(fp);
    free(str->s);
    free(str);
    *_n = n;
    return list;
}

static bam_header_t *hash2header(const kh_ref_t *hash)
{
    int i;
    bam_header_t *header;
    khiter_t k;

    header = bam_header_init();
    header->n_targets = kh_size(hash);
    header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
    header->target_len = (uint32_t*)calloc(kh_size(hash), 4);

    for (k=kh_begin(hash); k != kh_end(hash); ++k)
    {
        if (kh_exist(hash, k))
        {
            i = (int)kh_value(hash, k);
            header->target_name[i] = (char*)kh_key(hash, k);
            header->target_len[i] = kh_value(hash, k)>>32;
        }
    }
    bam_init_header_hash2(header);
    return header;
}

bam_header_t *sam_header_read2(const char *fn)
{
    bam_header_t *header;
    int i;
    int c;
    int dret;
    int ret;
    int len;
    int error = 0;
    char *s = NULL;
    gzFile fp;
    kstream_t *ks;
    kstring_t *str;
    kh_ref_t *hash;
    khiter_t k;

    if (fn == 0)
        return 0;
    fp = (strcmp(fn, "-") == 0) ? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
    if (fp == 0)
        return 0;
    hash = kh_init(ref);
    ks = ks_init(fp);
    str = (kstring_t*)calloc(1, sizeof(kstring_t));
    while (ks_getuntil(ks, 0, str, &dret) > 0)
    {
        s = strdup(str->s);
        i = kh_size(hash);
        ks_getuntil(ks, 0, str, &dret);
        len = atoi(str->s);
        k = kh_put(ref, hash, s, &ret);
        if (ret == 0)
        {
            fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
            error = 1;
        }
        kh_value(hash, k) = (uint64_t)len<<32 | i;
        if (dret != '\n')
            while ((c = ks_getc(ks)) != '\n' && c != -1);
    }
    ks_destroy(ks);
    gzclose(fp);
    free(str->s);
    free(str);
    fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
    if (error)
        return 0;
    header = hash2header(hash);
    kh_destroy(ref, hash);
    return header;
}

static inline uint8_t *alloc_data(bam1_t *b, int size)
{
    if (b->m_data < size)
    {
        b->m_data = size;
        kroundup32(b->m_data);
        b->data = (uint8_t*)realloc(b->data, b->m_data);
    }
    return b->data;
}

static inline void parse_error(int64_t n_lines, const char * __restrict msg)
{
    fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
    abort();
}

static inline void append_text(bam_header_t *header, kstring_t *str)
{
    size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
    kroundup32(x);
    kroundup32(y);
    if (x < y)
    {
        header->n_text = y;
        header->text = (char*)realloc(header->text, y);
        if (!header->text)
        {
            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
            abort();
        }
    }
    // Sanity check
    if (header->l_text+str->l+1 >= header->n_text)
    {
        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
        abort();
    }
    strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
    header->l_text += str->l + 1;
    header->text[header->l_text] = 0;
}

int sam_header_parse(bam_header_t *h)
{
    int i;
    char **tmp = NULL;

    free(h->target_len);
    free(h->target_name);
    h->n_targets = 0;
    h->target_len = 0;
    h->target_name = 0;
    if (h->l_text < 3)
        return 0;
    if (h->dict == 0)
        h->dict = sam_header_parse2(h->text);
    tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
    if (h->n_targets == 0)
        return 0;
    h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
    for (i=0; i < h->n_targets; ++i)
        h->target_name[i] = strdup(tmp[i]);
    free(tmp);
    tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
    h->target_len = (uint32_t*)calloc(h->n_targets, 4);
    for (i=0; i < h->n_targets; ++i)
        h->target_len[i] = atoi(tmp[i]);
    free(tmp);
    return h->n_targets;
}

void bam_init_header_hash2(bam_header_t *header)
{
    int i;

    if (header->hash == 0)
    {
        int ret = 0;
        khiter_t iter;
        khash_t(s) *h;

        header->hash = h = kh_init(s);
        for (i=0; i < header->n_targets; ++i)
        {
            iter = kh_put(s, h, header->target_name[i], &ret);
            kh_value(h, iter) = i;
        }
    }
}

bam_header_t *sam_header_read(tamFile fp)
{
    int ret;
    int dret;
    bam_header_t *header = bam_header_init();
    kstring_t *str = fp->str;

    while (((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0) && (str->s[0] == '@'))
    {
        // skip header
        str->s[str->l] = dret; // note that str->s is NOT null terminated!!
        append_text(header, str);
        if (dret != '\n')
        {
            ret = ks_getuntil(fp->ks, '\n', str, &dret);
            str->s[str->l] = '\n'; // NOT null terminated!!
            append_text(header, str);
        }
        ++fp->n_lines;
    }
    sam_header_parse(header);
    bam_init_header_hash2(header);
    fp->is_first = 1;
    return header;
}

int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
{
    int ret;
    int doff;
    int doff0;
    int dret;
    int z = 0;
    bam1_core_t *c = &b->core;
    kstring_t *str = fp->str;
    kstream_t *ks = fp->ks;

    if (fp->is_first)
    {
        fp->is_first = 0;
        ret = str->l;
    }
    else
    {
        do
        {
            // special consideration for empty lines
            ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
            if (ret >= 0)
                z += str->l + 1;
        }
        while (ret == 0);
    }
    if (ret < 0)
        return -1;
    ++fp->n_lines;
    doff = 0;

    {
        // name
        c->l_qname = strlen(str->s) + 1;
        memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
        doff += c->l_qname;
    }
    {
        // flag
        long flag;
        char *s = NULL;
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        flag = strtol((char*)str->s, &s, 0);
        if (*s)
        {
            // not the end of the string
            flag = 0;
            for (s=str->s; *s; ++s)
                flag |= bam_char2flag_table[(int)*s];
        }
        c->flag = flag;
    }
    {
        // tid, pos, qual
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->tid = bam_get_tid(header, str->s);
        if ((c->tid < 0) && (strcmp(str->s, "*")))
        {
            if (header->n_targets == 0)
            {
                fprintf(stderr, "[sam_read1] missing header? Abort!\n");
                exit(1);
            }
            else
                fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
        }
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->pos = isdigit(str->s[0]) ? atoi(str->s) - 1 : -1;
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->qual = isdigit(str->s[0]) ? atoi(str->s) : 0;
        if (ret < 0)
            return -2;
    }
    {
        // cigar
        char *s = NULL;
        char *t = NULL;
        int i;
        int op;
        long x;
        c->n_cigar = 0;
        if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0)
            return -3;
        z += str->l + 1;
        if (str->s[0] != '*')
        {
            uint32_t *cigar = NULL;
            for (s=str->s; *s; ++s)
            {
                if ((isalpha(*s)) || (*s=='='))
                    ++c->n_cigar;
                else if (!isdigit(*s))
                    parse_error(fp->n_lines, "invalid CIGAR character");
            }
            b->data = alloc_data(b, doff + c->n_cigar * 4);
            cigar = bam1_cigar(b);
            for (i=0, s=str->s; i != c->n_cigar; ++i)
            {
                x = strtol(s, &t, 10);
                op = toupper(*t);
                if (op == 'M')
                    op = BAM_CMATCH;
                else if (op == 'I')
                    op = BAM_CINS;
                else if (op == 'D')
                    op = BAM_CDEL;
                else if (op == 'N')
                    op = BAM_CREF_SKIP;
                else if (op == 'S')
                    op = BAM_CSOFT_CLIP;
                else if (op == 'H')
                    op = BAM_CHARD_CLIP;
                else if (op == 'P')
                    op = BAM_CPAD;
                else if (op == '=')
                    op = BAM_CEQUAL;
                else if (op == 'X')
                    op = BAM_CDIFF;
                else if (op == 'B')
                    op = BAM_CBACK;
                else
                    parse_error(fp->n_lines, "invalid CIGAR operation");
                s = t + 1;
                cigar[i] = bam_cigar_gen(x, op);
            }
            if (*s)
                parse_error(fp->n_lines, "unmatched CIGAR operation");
            c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
            doff += c->n_cigar * 4;
        }
        else
        {
            if (!(c->flag & BAM_FUNMAP))
            {
                fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
                c->flag |= BAM_FUNMAP;
            }
            c->bin = bam_reg2bin(c->pos, c->pos + 1);
        }
    }
    {
        // mtid, mpos, isize
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->mtid = strcmp(str->s, "=") ? bam_get_tid(header, str->s) : c->tid;
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->mpos = isdigit(str->s[0]) ? atoi(str->s) - 1 : -1;
        ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret);
        z += str->l + 1;
        c->isize = ((str->s[0] == '-') || (isdigit(str->s[0]))) ? atoi(str->s) : 0;
        if (ret < 0)
            return -4;
    }
    {
        // seq and qual
        int i;
        unsigned char *p = NULL;
        if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0)
            return -5; // seq
        z += str->l + 1;
        if (strcmp(str->s, "*"))
        {
            c->l_qseq = strlen(str->s);
            if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
            {
                fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
                        (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
                parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
            }
            p = (unsigned char*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
            memset(p, 0, (c->l_qseq+1)/2);
            for (i=0; i < c->l_qseq; ++i)
                p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
        }
        else
            c->l_qseq = 0;
        if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0)
            return -6; // qual
        z += str->l + 1;
        if (strcmp(str->s, "*") && (c->l_qseq != strlen(str->s)))
            parse_error(fp->n_lines, "sequence and quality are inconsistent");
        p += (c->l_qseq+1)/2;
        if (strcmp(str->s, "*") == 0)
            for (i=0; i < c->l_qseq; ++i)
                p[i] = 0xff;
        else
            for (i=0; i < c->l_qseq; ++i)
                p[i] = str->s[i] - 33;
        doff += c->l_qseq + (c->l_qseq+1)/2;
    }
    doff0 = doff;
    if ((dret != '\n') && (dret != '\r'))
    {
        // aux
        while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0)
        {
            uint8_t *s;
            uint8_t type;
            uint8_t key[2];
            z += str->l + 1;
            if ((str->l < 6) || (str->s[2] != ':') || (str->s[4] != ':'))
                parse_error(fp->n_lines, "missing colon in auxiliary data");
            key[0] = str->s[0];
            key[1] = str->s[1];
            type = str->s[3];
            s = alloc_data(b, doff + 3) + doff;
            s[0] = key[0];
            s[1] = key[1];
            s += 2;
            doff += 2;
            if ((type == 'A') || (type == 'a') || (type == 'c') || (type == 'C'))
            {
                // c and C for backward compatibility
                s = alloc_data(b, doff + 2) + doff;
                *s++ = 'A';
                *s = str->s[5];
                doff += 2;
            }
            else if ((type == 'I') || (type == 'i'))
            {
                long long x;
                s = alloc_data(b, doff + 5) + doff;
                x = (long long)atoll(str->s + 5);
                if (x < 0)
                {
                    if (x >= -127)
                    {
                        *s++ = 'c';
                        *(int8_t*)s = (int8_t)x;
                        s += 1;
                        doff += 2;
                    }
                    else if (x >= -32767)
                    {
                        *s++ = 's';
                        *(int16_t*)s = (int16_t)x;
                        s += 2;
                        doff += 3;
                    }
                    else
                    {
                        *s++ = 'i';
                        *(int32_t*)s = (int32_t)x;
                        s += 4;
                        doff += 5;
                        if (x < -2147483648ll)
                            fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
                                    (long long)fp->n_lines, x);
                    }
                }
                else
                {
                    if (x <= 255)
                    {
                        *s++ = 'C';
                        *s++ = (uint8_t)x;
                        doff += 2;
                    }
                    else if (x <= 65535)
                    {
                        *s++ = 'S';
                        *(uint16_t*)s = (uint16_t)x;
                        s += 2;
                        doff += 3;
                    }
                    else
                    {
                        *s++ = 'I';
                        *(uint32_t*)s = (uint32_t)x;
                        s += 4;
                        doff += 5;
                        if (x > 4294967295ll)
                            fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
                                    (long long)fp->n_lines, x);
                    }
                }
            }
            else if (type == 'f')
            {
                s = alloc_data(b, doff + 5) + doff;
                *s++ = 'f';
                *(float*)s = (float)atof(str->s + 5);
                s += 4;
                doff += 5;
            }
            else if (type == 'd')
            {
                s = alloc_data(b, doff + 9) + doff;
                *s++ = 'd';
                *(float*)s = (float)atof(str->s + 9);
                s += 8;
                doff += 9;
            }
            else if ((type == 'Z') || (type == 'H'))
            {
                int size = 1 + (str->l - 5) + 1;
                if (type == 'H')
                {
                    // check whether the hex string is valid
                    int i;
                    if ((str->l - 5) % 2 == 1)
                        parse_error(fp->n_lines, "length of the hex string not even");
                    for (i=0; i < str->l - 5; ++i)
                    {
                        int c = toupper(str->s[5 + i]);
                        if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
                            parse_error(fp->n_lines, "invalid hex character");
                    }
                }
                s = alloc_data(b, doff + size) + doff;
                *s++ = type;
                memcpy(s, str->s + 5, str->l - 5);
                s[str->l - 5] = 0;
                doff += size;
            }
            else if (type == 'B')
            {
                int32_t n = 0, Bsize, k = 0, size;
                char *p;
                if (str->l < 8)
                    parse_error(fp->n_lines, "too few values in aux type B");
                Bsize = bam_aux_type2size(str->s[5]); // the size of each element
                for (p=(char*)str->s + 6; *p; ++p) // count the number of elements in the array
                    if (*p == ',')
                        ++n;
                p = str->s + 7; // now p points to the first number in the array
                size = 6 + Bsize * n; // total number of bytes allocated to this tag
                s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
                *s++ = 'B';
                *s++ = str->s[5];
                memcpy(s, &n, 4);
                s += 4;
                // write the number of elements
                if (str->s[5] == 'c')
                    while (p < str->s + str->l)
                        ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
                else if (str->s[5] == 'C')
                    while (p < str->s + str->l)
                        ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
                else if (str->s[5] == 's')
                    while (p < str->s + str->l)
                        ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
                else if (str->s[5] == 'S')
                    while (p < str->s + str->l)
                        ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
                else if (str->s[5] == 'i')
                    while (p < str->s + str->l)
                        ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
                else if (str->s[5] == 'I')
                    while (p < str->s + str->l)
                        ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
                else if (str->s[5] == 'f')
                    while (p < str->s + str->l)
                        ((float*)s)[k++] = (float)strtod(p, &p), ++p;
                else
                    parse_error(fp->n_lines, "unrecognized array type");
                s += Bsize * n;
                doff += size;
            }
            else
                parse_error(fp->n_lines, "unrecognized type");
            if (dret == '\n' || dret == '\r')
                break;
        }
    }
    b->l_aux = doff - doff0;
    b->data_len = doff;
    if (bam_no_B)
        bam_remove_B(b);
    return z;
}

tamFile sam_open(const char *fn)
{
    tamFile fp;
    gzFile gzfp = (strcmp(fn, "-") == 0) ? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
    if (gzfp == 0)
        return 0;
    fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
    fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
    fp->fp = gzfp;
    fp->ks = ks_init(fp->fp);
    return fp;
}

void sam_close(tamFile fp)
{
    if (fp)
    {
        ks_destroy(fp->ks);
        gzclose(fp->fp);
        free(fp->str->s);
        free(fp->str);
        free(fp);
    }
}