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io.c
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/*******************************************************************************************
*
* A module adapted from the VGPseq library (written by me). This input module can
* read fasta, fastq, sam, bam, and cram files along with Dazzler db's and dam's.
* Given a target # of threads ITHREADS, it first finds partition points in the input file
* that split the file into the required # of parts:
*
* Input_Partition *Partition_Input(int argc, char *argv[])
*
* It can then either supply a single large training block:
*
* DATA_BLOCK *Get_First_Block(Input_Partition *parts, int64 numbp)
*
* or in a thread parallel manner read each partition and transmit it in DATA_BLOCKs to a
* given call-back routine:
*
* void Scan_All_Input(Input_Partition *parts)
*
* Author: Gene Myers
* Date: October 2020
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <stdint.h>
#include <ctype.h>
#include <time.h>
#include <pthread.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <stdbool.h>
#include "libfastk.h"
#include "FastK.h"
#include "LIBDEFLATE/libdeflate.h"
#include "HTSLIB/htslib/hts.h"
#include "HTSLIB/htslib/hfile.h"
#include "HTSLIB/cram/cram.h"
#include <zlib.h>
#undef DEBUG_FIND
#undef DEBUG_IO
#undef DEBUG_TRAIN
#undef DEBUG_OUT
#undef DEBUG_AUTO
#undef DEBUG_BAM_IO
#undef DEBUG_BAM_RECORD
#ifdef DEBUG_OUT
#define CALL_BACK Print_Block
#else
#define CALL_BACK Distribute_Block
#endif
#define IO_BLOCK 10000000ll
#define DT_BLOCK 1000000ll
#define DT_MINIM 100000ll
#define DT_READS 10000
typedef struct libdeflate_decompressor DEPRESS;
#define INT_MAXLEN 10
#define CRAM 0
#define BAM 1
#define SAM 2
#define FASTQ 3
#define FASTA 4
#define DAZZ 5
static char *Tstring[7] = { "cram", "bam", "sam", "fastq", "fasta", "db", "dam" };
typedef struct
{ char *path; // Full path name
char *root; // Ascii root name
char *pwd; // Ascii path name
int64 fsize; // Size of file in bytes
int ftype; // Type of file
int zipd; // Is file gzip'd
int64 zsize; // Size of compression index for cram and dazz
int64 *zoffs; // zoffs[i] = offset to compressed block i
int DB_all; // Trim parameters for Dazzler DB's
int DB_cut;
} File_Object;
typedef struct
{ int64 fpos; // offset in source file of desired unit (gzip block, cram contaianer)
uint32 boff; // offset within a unit block of desired record
} Location;
#define SAMPLE 0
#define SPLIT 1
typedef struct
{ File_Object *fobj; // array of file objects
uint8 *buf; // block buffer
int fid; // fid of fobj[bidx].path
int bidx; // Scan range is [bidx:beg,eidx:end)
Location beg;
int eidx;
Location end;
int action; // sampling or splitting
int64 work; // total sizes of all files
DATA_BLOCK block; // block buffer for this thread
int thread_id; // thread index (in [0,NTHREAD-1]
void * (*output_thread)(void *); // output routine for file type
DEPRESS *decomp; // decompressor
} Thread_Arg;
static void do_nothing(Thread_Arg *parm)
{ (void) parm; }
/*******************************************************************************************
*
* Routines to open and close the sequence file types supported
*
********************************************************************************************/
// Open and get info about each input file
static int64 *genes_cram_index(char *path, int64 fsize, int64 *zsize);
static void read_DB_stub(char *path, int *cut, int *all);
static int64 *get_dazz_offsets(FILE *idx, int64 *zsize);
static void Fetch_File(char *arg, File_Object *input, int gz_ok)
{ static char *suffix[] = { ".cram", ".bam", ".sam", ".db", ".dam",
".fastq", ".fasta", ".fq", ".fa",
".fastq.gz", ".fasta.gz", ".fastq", ".fasta",
".fq.gz", ".fa.gz", ".fq", ".fa" };
static char *extend[] = { ".cram", ".bam", ".sam", ".db", ".dam",
".fastq", ".fasta", ".fq", ".fa",
".fastq.gz", ".fasta.gz", ".fastq.gz", ".fasta.gz",
".fq.gz", ".fa.gz", ".fq.gz", ".fa.gz" };
struct stat stats;
char *pwd, *root, *path, *temp;
int fid, i;
int64 fsize, zsize, *zoffs;
int ftype, zipd;
pwd = PathTo(arg);
for (i = 0; i < 17; i++)
{ root = Root(arg,suffix[i]);
fid = open(Catenate(pwd,"/",root,extend[i]),O_RDONLY);
if (fid >= 0) break;
free(root);
}
if (fid < 0)
{ fprintf(stderr,"\n%s: Cannot open %s as a .cram|[bs]am|f{ast}[aq][.gz]|db|dam file\n",
Prog_Name,arg);
Clean_Exit(1);
}
if (i == 3 || i == 4)
{ ftype = DAZZ;
zipd = 0;
}
else if (i >= 5)
{ ftype = FASTA - (i%2);
zipd = (i >= 9);
}
else
{ ftype = i;
zipd = 0;
}
path = Strdup(Catenate(pwd,"/",root,extend[i]),"Allocating full path name");
zoffs = NULL;
if (zipd)
{ if (gz_ok)
{ if (stat(path,&stats) == -1)
{ fprintf(stderr,"\n%s: Cannot get stats for %s\n",Prog_Name,path);
Clean_Exit(1);
}
fsize = stats.st_size;
zsize = (fsize-1)/IO_BLOCK+1;
}
else
{ if (VERBOSE)
fprintf(stderr," Gzipped file %s being temporarily uncompressed\n",arg);
temp = Strdup(Catenate(SORT_PATH,"/",root,extend[i]),"Allocating full path name");
temp[strlen(temp)-3] = '\0';
system(Catenate("gunzip -c ",path," >",temp));
free(path);
path = temp;
zipd = 0;
if (stat(path,&stats) == -1)
{ fprintf(stderr,"\n%s: Cannot get stats for %s\n",Prog_Name,path);
Clean_Exit(1);
}
fsize = stats.st_size;
zsize = (fsize-1)/IO_BLOCK+1;
}
}
else if (ftype == DAZZ)
{ FILE *idx;
read_DB_stub(path,&(input->DB_cut),&(input->DB_all));
free(path);
close(fid);
path = Strdup(Catenate(pwd,"/.",root,".bps"),"Allocating full path name");
fid = open(path,O_RDONLY);
if (fid < 0)
{ fprintf(stderr,"\n%s: Dazzler DB %s does not have a .bps file ! ?\n",Prog_Name,root);
Clean_Exit(1);
}
if (fstat(fid, &stats) == -1)
{ fprintf(stderr,"\n%s: Cannot get stats for %s\n",Prog_Name,arg);
Clean_Exit(1);
}
fsize = stats.st_size;
idx = fopen(Catenate(pwd,"/.",root,".idx"),"r");
if (idx == NULL)
{ fprintf(stderr,"\n%s: Dazzler DB %s does not have a .idx file ! ?\n",Prog_Name,root);
Clean_Exit(1);
}
zoffs = get_dazz_offsets(idx,&zsize);
zoffs[zsize] = fsize;
fclose(idx);
}
else
{ if (fstat(fid, &stats) == -1)
{ fprintf(stderr,"\n%s: Cannot get stats for %s\n",Prog_Name,arg);
Clean_Exit(1);
}
fsize = stats.st_size;
if (ftype == CRAM)
zoffs = genes_cram_index(path,fsize,&zsize);
else
zsize = (fsize-1)/IO_BLOCK+1;
}
#ifdef DEBUG_FIND
fprintf(stderr,"\n%s is a %s file, ftype = %d, zipd = %d, fsize = %lld\n",
arg,suffix[i],ftype,zipd,fsize);
#endif
close(fid);
input->path = path;
input->root = root;
input->pwd = pwd;
input->fsize = fsize;
input->ftype = ftype;
input->zipd = zipd;
input->zsize = zsize;
input->zoffs = zoffs;
}
static void Free_File(File_Object *input, int gz_ok)
{ if (!gz_ok && input->zipd)
unlink(input->path);
free(input->zoffs);
free(input->path);
free(input->root);
free(input->pwd);
}
/*******************************************************************************************
*
* DATA_BLOCK CODE
*
********************************************************************************************/
static int homo_compress(char *seq, int len)
{ int i, x, n;
n = 0;
x = seq[n++];
for (i = 1; i < len; i++)
if (seq[i] != x)
seq[n++] = x = seq[i];
seq[n] = '\0';
return (n);
}
static int Add_Data_Block(DATA_BLOCK *dset, int len, char *seq)
{ int n, r;
int64 o;
r = 0;
n = dset->nreads;
o = dset->boff[n];
if (dset->rem > 0)
{ len = dset->rem;
seq = dset->next;
}
else if (COMPRESS)
len = homo_compress(seq,len);
if (n >= dset->maxrds)
return (1);
if (o+len >= dset->maxbps)
{ if (dset->maxbps-o > DT_MINIM)
{ r = 1;
dset->rem = len;
len = (dset->maxbps-o);
dset->rem -= (len - (KMER-1));
dset->next = seq + (len - (KMER-1));
}
else
return (1);
}
else
dset->rem = 0;
dset->nreads = ++n;
memcpy(dset->bases+o,seq,len);
o += len;
dset->bases[o] = '\0';
dset->boff[n] = o+1;
dset->totlen += len;
return (r);
}
#if defined(DEBUG_OUT) || defined(DEBUG_TRAIN)
static void Print_Block(DATA_BLOCK *dset, int tid)
{ int64 end;
int i;
char *bases;
static int tc = 0;
(void) tid;
printf("Buffer load rem = %d\n",dset->rem);
bases = dset->bases;
for (i = 0; i < dset->nreads; i++)
{ end = dset->boff[i+1]-1;
printf("%5d %8d:\n",i,tc++);
#undef ONE_LINE
#ifdef ONE_LINE
printf(" %.80s\n",bases+dset->boff[i]);
#else
{ int64 j;
for (j = dset->boff[i]; j+80 < end; j += 80)
printf(" %.80s\n",bases+j);
if (j < end)
printf(" %.*s\n",(int) (end-j),bases+j);
}
#endif
}
fflush(stdout);
}
#endif
static void Reset_Data_Block(DATA_BLOCK *dset, int roll)
{ if (roll)
{ memcpy(dset->bases,dset->bases+(dset->boff[dset->nreads]-KMER),KMER-1);
dset->totlen = KMER-1;
}
else
dset->totlen = 0;
dset->nreads = 0;
dset->boff[0] = 0;
}
/*******************************************************************************************
*
* FASTA / FASTQ SPECIFIC CODE
*
********************************************************************************************/
/*******************************************************************************************
*
* fast_nearest: Routine to find next entry given arbitray start point.
*
********************************************************************************************/
// Automata states (buffer is processed char at a time)
#define UK 0
#define FK 1
#define FK1 2
#if defined(DEBUG_AUTO)
static char *Name[] =
{ "UK", "FK", "FK1", "QHL" };
#endif
// Check blocks [beg,end) starting with the first complete entry and proceeding
// into blocks end ... if necessary to complete the last entry started in this
// range.
static void fast_nearest(Thread_Arg *data)
{ int fid = data->fid;
int64 beg = data->beg.fpos;
uint8 *buf = data->buf;
File_Object *inp = data->fobj + data->bidx;
int fastq = (inp->ftype == FASTQ);
int64 blk, off;
int slen;
int state;
int nl_1, nl_2, pl_1, alive;
int b, c;
#ifdef DEBUG_FIND
fprintf(stderr,"\nFind starting at %lld\n",beg);
#endif
blk = beg / IO_BLOCK;
off = beg % IO_BLOCK;
lseek(fid,blk*IO_BLOCK,SEEK_SET);
if (fastq)
state = UK;
else
state = FK;
nl_1 = pl_1 = nl_2 = 1;
alive = 0;
#ifdef DEBUG_FIND
fprintf(stderr,"\nFrom block %lld / offset %lld\n",blk,off);
#endif
while (blk < inp->zsize)
{
#ifdef DEBUG_FIND
fprintf(stderr," Loading block %lld: @%lld",blk,lseek(fid,0,SEEK_CUR));
#endif
slen = read(fid,buf,IO_BLOCK);
#ifdef DEBUG_FIND
fprintf(stderr," %d %d\n",slen,errno);
#endif
for (b = off; b < slen; b++)
{ c = buf[b];
#ifdef DEBUG_AUTO
fprintf(stderr," %.5s: %c\n",Name[state],c);
#endif
switch (state)
{ case UK:
if (c == '@' && alive)
{ data->beg.fpos = blk*IO_BLOCK + b;
data->beg.boff = 0;
return;
}
alive = (c == '\n' && ! (nl_2 || pl_1));
nl_2 = nl_1;
nl_1 = (c == '\n');
pl_1 = (c == '+');
#ifdef DEBUG_AUTO
fprintf(stderr," n2=%d n1=%d p1=%d a=%d\n",nl_2,nl_1,pl_1,alive);
#endif
break;
case FK:
if (c == '\n')
state = FK1;
break;
case FK1:
if (c == '>')
{ data->beg.fpos = blk*IO_BLOCK + b;
data->beg.boff = 0;
return;
}
else if (c != '\n')
state = FK;
break;
}
}
blk += 1;
off = 0;
}
data->beg.fpos = -1;
data->beg.boff = 0;
return;
}
/*******************************************************************************************
*
* Second pass thread routines prepare .seq formated output in buffers for each input block.
* Note carefully that there are separate blocks for the forward and reverse files if
* processing a pair, the reads in the blocks need to be paired.
*
********************************************************************************************/
// Automata states (buffer is processed char at a time)
#define QAT 0
#define HSKP 1
#define QSEQ 2
#define QPLS 3
#define QSKP 4
#define ASEQ 5
#define AEOL 6
#if defined(DEBUG_AUTO)
static char *Name2[] =
{ "QAT", "HEAD", "HSKP", "QSEQ", "QPLS", "QSKP", "QQVS", "ASEQ", "AEOL" };
#endif
#define DUMP(scale,notyet,dclose) \
if (action == SAMPLE) \
{ dset->ratio = ((1.*parm->work) / (totread-(notyet))) * scale; \
dset->totlen = dset->boff[dset->nreads] - dset->nreads; \
dclose(fid); \
return (NULL); \
} \
else \
{ dset->totlen = dset->boff[dset->nreads] - dset->nreads; \
CALL_BACK(dset,tid); \
if (CLOCK) \
{ cumbps += dset->totlen; \
if (cumbps >= nxtbps) \
{ fprintf(stderr,"\r %3d%%",(int) ((100.*cumbps)/estbps)); \
fflush(stderr); \
nxtbps = cumbps+pct1; \
} \
} \
} \
#define END_SEQ(notyet) \
{ line[olen++] = lastc = '\0'; \
dset->boff[++dset->nreads] = olen; \
if (olen > omax-DT_MINIM || dset->nreads >= dset->maxrds) \
{ DUMP(ratio,notyet,close) \
Reset_Data_Block(dset,0); \
olen = 0; \
} \
}
#define ADD(c) \
{ if (!COMPRESS || c != lastc) \
{ if (olen >= omax) \
{ line[olen++] = '\0'; \
dset->boff[++dset->nreads] = olen; \
dset->rem = 1; \
DUMP(ratio,slen-b,close) \
dset->rem = 0; \
Reset_Data_Block(dset,1); \
olen = KMER-1; \
} \
line[olen++] = lastc = c; \
} \
}
// Write fast records in relevant partition
static void *fast_output_thread(void *arg)
{ Thread_Arg *parm = (Thread_Arg *) arg;
File_Object *fobj = parm->fobj;
uint8 *buf = parm->buf;
int action = parm->action;
DATA_BLOCK *dset = &parm->block;
int tid = parm->thread_id;
int fastq = (fobj->ftype == FASTQ); // Is the same for all files (already checked)
File_Object *inp;
int f, fid;
gzFile gzid = NULL;
int64 blk, off;
int64 epos, eblk, eoff;
int64 totread;
double ratio;
int state, lastc;
int omax, olen;
char *line;
int64 estbps, cumbps, nxtbps, pct1;
int CLOCK;
estbps = nxtbps = pct1 = cumbps = 0;
if (VERBOSE && tid == 0 && action != SAMPLE)
{ estbps = dset->ratio / ITHREADS;
nxtbps = pct1 = estbps/100;
fprintf(stderr,"\n 0%%");
fflush(stderr);
CLOCK = 1;
}
else
CLOCK = 0;
// Do relevant section of each file assigned to this thread in sequence
omax = dset->maxbps;
line = dset->bases;
totread = 0;
olen = 0;
ratio = 1.;
for (f = parm->bidx; f <= parm->eidx; f++)
{ inp = fobj+f;
fid = open(inp->path,O_RDONLY);
if (f < parm->eidx)
epos = inp->fsize;
else
epos = parm->end.fpos;
if (f > parm->bidx)
parm->beg.fpos = 0;
#ifdef DEBUG_IO
fprintf(stderr,"Block: %12lld to %12lld --> %8lld\n",
parm->beg.fpos,epos,epos - parm->beg.fpos);
fflush(stdout);
#endif
blk = parm->beg.fpos / IO_BLOCK;
off = parm->beg.fpos % IO_BLOCK;
eblk = (epos-1) / IO_BLOCK;
eoff = (epos-1) % IO_BLOCK + 1;
if (inp->zipd)
{ gzid = gzdopen(fid,"r");
eblk = 0x7fffffffffffffffll;
}
else
lseek(fid,blk*IO_BLOCK,SEEK_SET);
state = QAT;
lastc = 0;
#ifdef DEBUG_IO
fprintf(stderr,"\nFrom block %lld / offset %lld\n",blk,off);
#endif
while (blk <= eblk)
{ int c, b, slen;
#ifdef DEBUG_IO
fprintf(stderr," Loading block %lld: @%lld",blk,lseek(fid,0,SEEK_CUR));
#endif
if (inp->zipd)
{ slen = gzread(gzid,buf,IO_BLOCK);
if (blk == 0 && slen != 0 && action == SAMPLE)
ratio = (1.*slen) / gzoffset(gzid);
}
else
slen = read(fid,buf,IO_BLOCK);
if (slen == 0)
break;
totread += slen;
#ifdef DEBUG_IO
fprintf(stderr," %d\n",slen);
#endif
if (blk == eblk && eoff < slen)
slen = eoff;
for (b = off; b < slen; b++)
{ c = buf[b];
#ifdef DEBUG_AUTO
fprintf(stderr," %.5s: %c\n",Name2[state],c);
#endif
switch (state)
{ case QAT:
state = HSKP;
break;
case HSKP:
if (c == '\n')
{ if (fastq)
state = QSEQ;
else
state = ASEQ;
}
break;
case QSEQ:
if (c != '\n')
ADD(c)
else
{ END_SEQ(slen-b)
state = QPLS;
}
break;
case QPLS:
if (c == '\n')
state = QSKP;
break;
case QSKP:
if (c == '\n')
state = QAT;
break;
case AEOL:
if (c == '>')
{ END_SEQ(slen-b)
state = HSKP;
}
else if (c != '\n')
{ ADD(c)
state = ASEQ;
}
break;
case ASEQ:
if (c == '\n')
state = AEOL;
else
ADD(c)
}
}
blk += 1;
off = 0;
}
if (state == AEOL)
END_SEQ(0)
if (inp->zipd)
gzclose_r(gzid);
else
close(fid);
}
dset->totlen = dset->boff[dset->nreads] - dset->nreads;
if (action == SAMPLE)
{ dset->ratio = ((1.*parm->work) / totread) * ratio;
return (NULL);
}
else if (dset->nreads > 0)
CALL_BACK(dset,tid);
if (CLOCK)
fprintf(stderr,"\r \r");
return (NULL);
}
/*******************************************************************************************
*
* BAM/SAM SPECIFIC CODE
*
********************************************************************************************/
#define BAM_BLOCK 0x10000
#define HEADER_LEN 36
#define SEQ_RUN 40
static int DNA[256] =
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
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, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
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, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
};
// Get value of little endian integer of n-bytes
static inline uint32 getint(uint8 *buf, int n)
{ uint32 val;
int k;
val = 0;
for (k = n-1; k >= 0; k--)
val = (val << 8) | buf[k];
return (val);
}
// Next len chars are printable and last is zero?
static inline int valid_name(char *name, int len)
{ int i;
if (len < 1)
return (0);
len -= 1;
for (i = 0; i < len; i++)
if ( ! isprint(name[i]))
return (0);
return (name[len] == 0);
}
// Next len ints are plausible cigar codes
static inline int valid_cigar(int32 *cigar, int len, int range)
{ int i, c;
for (i = 0; i < len; i++)
{ c = cigar[i];
if ((c & 0xf) > 8)
return (0);
c >>= 4;
if (c < 0 || c > range)
return (0);
}
return (1);
}
/*******************************************************************************************
*
* Routines to manage a BAM_FILE stream object
*
********************************************************************************************/
// Open BAM stream where compressed block start is known. Compressed BAM blocks are buffered
// in a very big IO buffer and the current uncompressed block is in a 64Kbp array.
typedef struct
{ int fid; // file descriptor
int last; // last block of data in file has been read
uint8 *buf; // IO buffer (of IO_BLOCK bytes, supplied by caller)
int blen; // # of bytes currently in IO buffer
int bptr; // start of next BAM block in IO buffer
uint8 bam[BAM_BLOCK+1]; // uncompressed bam block
uint32 bsize; // length of compressed bam block
uint32 ssize; // length of uncompressed bam block
Location loc; // current location in bam file
DEPRESS *decomp;
} BAM_FILE;
// Load next len bytes of uncompressed BAM data into array data
static void bam_get(BAM_FILE *file, uint8 *data, int len)
{ int chk, off;
uint8 *bam = file->bam;
int boff = file->loc.boff;
off = 0;
chk = file->ssize - boff;
while (len >= chk)
{ int bptr, blen, bsize;
uint8 *block, *buf;
uint32 ssize;
size_t tsize;
#ifdef DEBUG_BAM_IO
printf("Move %d bytes to data+%d from bam+%d\n",chk,off,boff);
#endif
if (data != NULL)
memcpy(data+off,bam+boff,chk);
off += chk;
len -= chk;
file->loc.fpos += file->bsize;
#ifdef DEBUG_BAM_IO
printf("File pos %lld\n",file->fpos);
#endif
if (chk == 0 && len == 0)
{ file->loc.boff = 0;
return;
}
buf = file->buf;
bptr = file->bptr;
blen = file->blen;
block = buf+bptr;
#ifdef DEBUG_BAM_IO
printf("Block at buffer %d\n",bptr);
#endif
while (bptr + 18 > blen || bptr + (bsize = getint(block+16,2) + 1) > blen)
{ chk = blen-bptr;
if (file->last)
{ fprintf(stderr,"\n%s: Corrupted BAM file\n",Prog_Name);
Clean_Exit(1);
}
memmove(buf,block,chk);
blen = chk + read(file->fid,buf+chk,IO_BLOCK-chk);
#ifdef DEBUG_BAM_IO
printf("Loaded %d to buf+%d for a total of %d\n",IO_BLOCK-chk,chk,blen);
#endif
if (blen < IO_BLOCK)
file->last = 1;
file->blen = blen;
bptr = 0;
block = buf;
}
// Fetch and uncompress next Bam block
if (libdeflate_gzip_decompress(file->decomp,block,bsize,bam,BAM_BLOCK,&tsize) != 0)
{ fprintf(stderr,"\n%s: Bad gzip block\n",Prog_Name);
Clean_Exit(1);
}
ssize = tsize;
boff = 0;
#ifdef DEBUG_BAM_IO
printf("Loaded gzip block of size %d into %d\n",bsize,ssize);
#endif
file->bsize = bsize;
file->ssize = ssize;
file->bptr = bptr + bsize;
chk = ssize;
}
#ifdef DEBUG_BAM_IO
printf("Xfer %d bytes to data+%d from bam+%d\n",len,off,boff);
#endif
if (data != NULL)
memcpy(data+off,bam+boff,len);
file->loc.boff = boff+len;
}
// Startup a bam stream, the location must be valid.
static void bam_start(BAM_FILE *file, int fid, uint8 *buf, Location *loc)
{ file->fid = fid;
file->ssize = 0;
file->bsize = 0;
file->buf = buf;
file->bptr = 0;
file->blen = 0;
file->last = 0;
lseek(fid,loc->fpos,SEEK_SET);
file->loc.fpos = loc->fpos;
file->loc.boff = 0;
bam_get(file,NULL,loc->boff);
}
static int bam_eof(BAM_FILE *file)
{ return (file->loc.boff == file->ssize && file->bptr == file->blen && file->last); }
/*******************************************************************************************
*
* Routines to manage a SAM stream, but as a BAM_FILE (only select fields are used)
*
********************************************************************************************/
// Get next line of SAM input if possible
static uint8 *sam_getline(BAM_FILE *file)
{ int rem;
int blen = file->blen;
int bptr = file->bptr;
uint8 *buf = file->buf;
uint8 *b, *d;
b = buf + bptr;
rem = blen-bptr;
if (rem == 0)
d = NULL;
else
d = memchr(b,'\n',rem);
if (d == NULL)
{ if (file->last)
{ fprintf(stderr,"\n%s: Corrupted SAM file",Prog_Name);
Clean_Exit(1);
}
memmove(buf,buf+bptr,rem);
blen = rem + read(file->fid,buf+rem,IO_BLOCK-rem);
if (blen < IO_BLOCK)
file->last = 1;
file->blen = blen;
bptr = 0;
b = buf;
d = memchr(b,'\n',blen);
if (d == NULL)
{ if (blen < IO_BLOCK)
fprintf(stderr,"\n%s: Corrupted SAM file",Prog_Name);
else
fprintf(stderr,"\n%s: SAM-line is longer than max %lld\n",Prog_Name,IO_BLOCK);
Clean_Exit(1);
}
}
d += 1;
file->bptr = d-buf;
file->loc.fpos += d-b;