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ONElib.c
3924 lines (3360 loc) · 115 KB
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ONElib.c
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/*****************************************************************************************
*
* file: ONElib.c
* implementation for ONElib.h
*
* Author: Richard Durbin (rd109@cam.ac.uk)
* Copyright (C) Richard Durbin, Cambridge University and Eugene Myers 2019-
*
* HISTORY:
* Last edited: Dec 4 23:57 2022 (rd109)
* * Apr 23 00:31 2020 (rd109): global rename of VGP to ONE, Vgp to One, vgp to one
* * Apr 20 11:27 2020 (rd109): added VgpSchema to make schema dynamic
* * Dec 27 09:46 2019 (gene): style edits + compactify code
* * Jul 8 04:28 2019 (rd109): refactored to use info[]
* * Created: Thu Feb 21 22:40:28 2019 (rd109)
*
****************************************************************************************/
#include <sys/errno.h>
#include <sys/types.h>
#include <stdlib.h>
#include <string.h>
#include <sys/resource.h>
#include <stdarg.h>
#include <time.h>
#include <ctype.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/uio.h>
#include <math.h>
#ifdef DEBUG
#include <assert.h>
#else
#define assert(x) 0
#endif
#include "ONElib.h"
// set major and minor code versions
#define MAJOR 1
#define MINOR 1
// utilities with implementation at the end of the file
static void die(char *format, ...); // print message to stderr and exit -1
static void *myalloc(size_t size); // allocate block, die if malloc fails
static void *mycalloc(size_t number, size_t size); // allocate & zero # objects of size
#define new(n,type) (type *) myalloc((n)*sizeof(type)) // actually use these not myalloc
#define new0(n,type) (type *) mycalloc((n),sizeof(type))
// global required for parallelisation
static pthread_mutex_t mutexInit = PTHREAD_MUTEX_INITIALIZER;
// forward declarations of serialisation functions lower in the file
// RD 220818: I think that many of int below should be I64, e.g. for len, ilen etc.
OneCodec *vcCreate();
void vcAddToTable(OneCodec *vc, int len, char *bytes);
void vcAddHistogram(OneCodec *vc, OneCodec *vh);
void vcCreateCodec(OneCodec *vc, int partial);
void vcDestroy(OneCodec *vc);
int vcMaxSerialSize();
int vcSerialize(OneCodec *vc, void *out);
OneCodec *vcDeserialize(void *in);
int vcEncode(OneCodec *vc, int ilen, char *ibytes, char *obytes);
int vcDecode(OneCodec *vc, int ilen, char *ibytes, char *obytes);
// forward declarations of 64-bit integer encoding/decoding
static inline int ltfWrite (I64 x, FILE *f) ;
static inline I64 ltfRead (FILE *f) ;
/***********************************************************************************
*
* ONE_FILE CREATION & DESTRUCTION
*
**********************************************************************************/
char* oneTypeString[] = { 0, "INT", "REAL", "CHAR", "STRING",
"INT_LIST", "REAL_LIST", "STRING_LIST", "DNA" } ;
/******************* OneInfo ********************/
static OneInfo *infoCreate (int nField)
{ OneInfo *vi = new0 (1, OneInfo) ;
vi->nField = nField ;
if (nField) vi->fieldType = new (nField, OneType) ;
return vi;
}
static OneInfo *infoDeepCopy (OneInfo *vi0)
{ OneInfo *vi = new (1, OneInfo) ;
*vi = *vi0 ;
if (vi->nField)
{ vi->fieldType = new (vi->nField, OneType) ;
memcpy (vi->fieldType, vi0->fieldType, vi->nField*sizeof(OneType)) ;
}
if (vi->listCodec && vi->listCodec != DNAcodec) vi->listCodec = vcCreate() ;
if (vi->comment) vi->comment = strdup (vi0->comment) ;
return vi ;
}
static bool infoCheckFields (OneInfo *vi, OneFile *vf)
{ // check field types against the STRING_LIST in vf
char *s = oneString(vf) ;
int i ;
if (vi->nField != oneLen(vf)) return false ;
for (i = 0 ; i < vi->nField ; ++i, s = oneNextString(vf,s))
if (strcmp (oneTypeString[vi->fieldType[i]], s)) return false ;
return true ;
}
static void infoDestroy (OneInfo *vi)
{ if (vi->buffer && ! vi->isUserBuf) free (vi->buffer) ;
if (vi->listCodec) vcDestroy (vi->listCodec) ;
if (vi->fieldType) free (vi->fieldType) ;
if (vi->comment) free (vi->comment) ;
free (vi);
}
/******************* OneSchema ********************/
// a utility to set the OneInfo list information
static int listEltSize[9] = { 0, 0, 0, 0, 1, sizeof(I64), sizeof(double), 1, 1 } ;
static void schemaAddInfoFromArray (OneSchema *vs, int n, OneType *a, char t, char type)
{
// use during the bootstrap, while parsing .def files, and while parsing ~ lines in other files
if (vs->info[(int) t])
die ("duplicate schema specification for linetype %c in filetype %s", t, vs->primary) ;
if (isalpha(t) && type == 'G')
{ if (vs->groupType) die ("second group type in schema for filetype %s", vs->primary) ;
vs->groupType = t ;
}
else if (isalpha(t) && type == 'O')
{ if (vs->objectType) die ("second object type in schema for filetype %s", vs->primary) ;
vs->objectType = t ;
}
else if (vs->primary && (type != 'D' || !isalpha(t))) // allow non-alphabetic lines in header
die ("non-alphabetic linetype %c (ascii %d) in schema for filetype %s",t,t,vs->primary) ;
if (n > vs->nFieldMax) vs->nFieldMax = n ;
OneInfo *vi = infoCreate (n) ;
memcpy (vi->fieldType, a, n*sizeof(OneType)) ;
int i ;
for (i = 0 ; i < n ; ++i)
if (a[i] >= oneSTRING)
{ if (vi->listEltSize)
die ("OneFile schema error; multiple list types for linetype definition %c", t) ;
vi->listEltSize = listEltSize[vi->fieldType[i]] ;
vi->listField = i ;
if (a[i] == oneDNA)
{ vi->listCodec = DNAcodec ; vi->isUseListCodec = true ; }
else
vi->listCodec = vcCreate () ; // always make a listCodec for any list type
}
if (t >= 'A' && t <= 'Z') vi->binaryTypePack = ((t-'A') << 1) | (char) 0x80 ;
else if (t >= 'a' && t <= 'z') vi->binaryTypePack = ((26+t-'a') << 1) | (char) 0x80 ;
else if (t == ';') vi->binaryTypePack = (52 << 2) | (char) 0x80 ;
else if (t == '&') vi->binaryTypePack = (53 << 2) | (char) 0x80 ;
else if (t == '*') vi->binaryTypePack = (54 << 2) | (char) 0x80 ;
else if (t == '/') vi->binaryTypePack = (55 << 2) | (char) 0x80 ;
else if (t == '.') vi->binaryTypePack = (56 << 2) | (char) 0x80 ;
vs->info[(int)t] = vi ;
}
static void schemaAddInfoFromLine (OneSchema *vs, OneFile *vf, char t, char type)
{ // assumes field specification is in the STRING_LIST of the current vf line
// need to set vi->comment separately
static OneType a[32] ;
int i ;
OneType j ;
char *s = oneString(vf) ;
int n = oneLen(vf) ;
if (n > 32)
die ("line specification %d fields too long - need to recompile", n) ;
for (i = 0 ; i < n ; ++i, s = oneNextString(vf,s))
{ a[i] = 0 ;
for (j = oneINT ; j <= oneDNA ; ++j)
if (!strcmp (s, oneTypeString[j])) a[i] = j ;
if (!a[i])
die ("ONE schema error: bad field %d of %d type %s in line %d type %c",
i, n, s, vf->line, t) ;
}
schemaAddInfoFromArray (vs, n, a, t, type) ;
if (oneReadComment (vf))
vs->info[(int)t]->comment = strdup (oneReadComment(vf)) ;
}
static OneSchema *schemaLoadRecord (OneSchema *vs, OneFile *vf)
{ char *s;
// parse a schema specfication line from vf and add into vs
// return value is vs unless a new primary type is declared, in which case vs->nxt
switch (vf->lineType)
{
case '.': // ignore - blank or comment line in schema file
break ;
case 'P':
if (vs->primary && !vs->objectType)
die ("schema: file type %s has no object type", vs->primary) ;
if (oneLen(vf) == 0) die ("schema: primary name must have at least one letter") ;
OneSchema *vsNxt = new0 (1, OneSchema) ;
vs->nxt = vsNxt ;
vs = vsNxt ;
s = oneString(vf);
vs->primary = new (oneLen(vf)+1, char) ;
strcpy (vs->primary, s) ;
vs->nFieldMax = 4 ; // needed for header
break ;
case 'S':
if (oneLen(vf) == 0) die ("schema: secondary name must have at least one letter") ;
if (vs->nSecondary)
{ char **temp = vs->secondary ;
vs->secondary = new (vs->nSecondary+1, char*) ;
memcpy (vs->secondary, temp, vs->nSecondary*sizeof(char*)) ;
free (temp) ;
}
else
vs->secondary = new (1, char*) ;
s = oneString(vf);
vs->secondary[vs->nSecondary] = new0 (oneLen(vf)+1, char) ;
strcpy (vs->secondary[vs->nSecondary++], s) ;
break ;
case 'G': // group type
case 'O': // object type
case 'D': // standard record type
schemaAddInfoFromLine (vs, vf, oneChar(vf,0), vf->lineType) ;
break ;
default:
die ("unrecognized schema line %d starting with %c", vf->line, vf->lineType) ;
}
return vs ;
}
static void oneFileDestroy (OneFile *vf) ; // need a forward declaration here
OneSchema *oneSchemaCreateFromFile (char *filename)
{
FILE *fs = fopen (filename, "r") ;
if (!fs) return 0 ;
fclose(fs);
OneSchema *vs = new0 (1, OneSchema) ;
OneFile *vf = new0 (1, OneFile) ; // shell object to support bootstrap
// bootstrap specification of linetypes to read schemas
{ OneInfo *vi ;
vi = vf->info['P'] = infoCreate (1) ; // to define the schema for parsing a .def file
vi->fieldType[0] = oneSTRING ; vi->listEltSize = 1 ; vi->listField = 0 ;
vi = vf->info['O'] = infoCreate (2) ; // object type specification
vi->fieldType[0] = oneCHAR ;
vi->fieldType[1] = oneSTRING_LIST ; vi->listEltSize = 1 ; vi->listField = 1 ;
vi = vf->info['D'] = infoCreate (2) ; // line type specification
vi->fieldType[0] = oneCHAR ;
vi->fieldType[1] = oneSTRING_LIST ; vi->listEltSize = 1 ; vi->listField = 1 ;
vf->info['/'] = infoCreate (0) ; // to store comments
vf->field = new (2, OneField) ;
}
// first load the universal header and footer (non-alphabetic) line types
// do this by writing their schema into a temporary file and parsing it into the base schema
{ errno = 0 ;
static char template[64] ;
#define VALGRIND_MACOS
#ifdef VALGRIND_MACOS // MacOS valgrind is missing functions to make temp files it seems
sprintf (template, "/tmp/OneSchema.%d", getpid()) ;
vf->f = fopen (template, "w+") ;
if (errno) die ("failed to open temporary file %s errno %d\n", template, errno) ;
#else
strcpy (template, "/tmp/OneSchema.XXXXXX") ;
int fd = mkstemp (template) ;
if (errno) die ("failed to open temporary file %s errno %d\n", template, errno) ;
vf->f = fdopen (fd, "w+") ;
if (errno) die ("failed to assign temporary file to stream: errno %d\n", errno) ;
#endif
unlink (template) ; // this ensures that the file is removed on closure
if (errno) die ("failed to remove temporary file %s errno %d\n", template, errno) ;
}
// NB if you change the header spec and add a record with more than 4 fields,
// change the assignment of ->nFieldMax in the 'P' section of schemaLoadRecord() above
fprintf (vf->f, "D 1 3 6 STRING 3 INT 3 INT first line: 3-letter type, major, minor version\n") ;
fprintf (vf->f, "D 2 1 6 STRING subtype: 3-letter subtype\n") ;
fprintf (vf->f, "D # 2 4 CHAR 3 INT linetype, count\n") ;
fprintf (vf->f, "D @ 2 4 CHAR 3 INT linetype, list max\n") ;
fprintf (vf->f, "D + 2 4 CHAR 3 INT linetype, list total\n") ;
fprintf (vf->f, "D %% 4 4 CHAR 4 CHAR 4 CHAR 3 INT group, #/+, linetype, value\n") ;
fprintf (vf->f, "D ! 1 11 STRING_LIST provenance: program, version, command, date\n") ;
fprintf (vf->f, "D < 2 6 STRING 3 INT reference: filename, object count\n") ;
fprintf (vf->f, "D > 1 6 STRING deferred: filename\n") ;
fprintf (vf->f, "D ~ 3 4 CHAR 4 CHAR 11 STRING_LIST embedded schema linetype definition\n") ;
fprintf (vf->f, "D . 0 blank line, anywhere in file\n") ;
fprintf (vf->f, "D $ 1 3 INT binary file - goto footer: isBigEndian\n") ;
fprintf (vf->f, "D ^ 0 binary file: end of footer designation\n") ;
fprintf (vf->f, "D - 1 3 INT binary file: offset of start of footer\n") ;
fprintf (vf->f, "D & 1 8 INT_LIST binary file: object index\n") ;
fprintf (vf->f, "D * 1 8 INT_LIST binary file: group index\n") ;
fprintf (vf->f, "D ; 2 4 CHAR 6 STRING binary file: list codec\n") ;
fprintf (vf->f, "D / 1 6 STRING binary file: comment\n") ;
if (fseek (vf->f, 0, SEEK_SET)) die ("ONE schema failure: cannot rewind tmp file") ;
while (oneReadLine (vf))
schemaLoadRecord (vs, vf) ;
// next reuse the temp file to load the schema for reading schemas
if (fseek (vf->f, 0, SEEK_SET)) die ("ONE schema failure: cannot rewind tmp file") ;
fprintf (vf->f, "P 3 def this is the primary file type for schemas\n") ;
fprintf (vf->f, "O P 1 6 STRING primary type name\n") ;
fprintf (vf->f, "D S 1 6 STRING secondary type name\n") ;
fprintf (vf->f, "D G 2 4 CHAR 11 STRING_LIST define linetype for groupType\n") ;
fprintf (vf->f, "D O 2 4 CHAR 11 STRING_LIST define linetype for objectType\n") ;
fprintf (vf->f, "D D 2 4 CHAR 11 STRING_LIST define linetype for other records\n") ;
fprintf (vf->f, "\n") ; // terminator
if (fseek (vf->f, 0, SEEK_SET)) die ("ONE schema failure: cannot rewind tmp file") ;
OneSchema *vs0 = vs ; // need this because loadInfo() updates vs on reading P lines
vf->line = 0 ;
while (oneReadLine (vf))
vs = schemaLoadRecord (vs, vf) ;
OneSchema *vsDef = vs ; // will need this to destroy it once the true schema is read
oneFileDestroy (vf) ; // this will also effectively remove the temp file on closing
// finally read the schema itself
if (!(vf = oneFileOpenRead (filename, vs0, "def", 1)))
return 0 ;
vs = vs0 ; // set back to vs0, so next filetype spec will replace vsDef
vs->nxt = 0 ;
oneSchemaDestroy (vsDef) ; // no longer need this, and can destroy because unlinked from vs0
while (oneReadLine (vf))
vs = schemaLoadRecord (vs, vf) ;
oneFileDestroy (vf) ;
return vs0 ;
}
static char *schemaFixNewlines (const char *text)
{ // replace literal "\n" by '\n' chars in text
char *newText = strdup (text) ;
char *s = newText, *t = s ;
while (*s)
if (*s == '\\' && s[1] == 'n')
{ *t++ = '\n' ; s += 2 ; }
else
*t++ = *s++ ;
*t = 0 ;
return newText ;
}
OneSchema *oneSchemaCreateFromText (char *text) // write to temp file and call CreateFromFile()
{
static char template[64] ;
sprintf (template, "/tmp/OneTextSchema-%d.def", getpid()) ;
errno = 0 ;
FILE *f = fopen (template, "w") ;
char *fixedText = schemaFixNewlines (text) ;
fprintf (f, "%s\n", fixedText) ;
free (fixedText) ;
fclose (f) ;
if (errno) die ("failed to write temporary file %s errno %d\n", template, errno) ;
OneSchema *vs = oneSchemaCreateFromFile (template) ;
errno = 0 ;
unlink (template) ; // delete temporary file - not ideal: will remain if schemaCreate crashes
if (errno) die ("failed to remove temporary file %s errno %d\n", template, errno) ;
return vs ;
}
static OneSchema *oneSchemaCreateDynamic (char *fileType, char *subType)
{ // this is clean, but it seems a bit wasteful to create a temp file
char text[32] ;
assert (fileType && strlen(fileType) > 0) ;
assert (!subType || strlen(subType) > 0) ;
if (subType)
sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
else
sprintf (text, "P %ld %s\n", strlen(fileType), fileType) ;
OneSchema *vs = oneSchemaCreateFromText (text) ;
return vs ;
}
void oneSchemaDestroy (OneSchema *vs)
{ int i ;
while (vs)
{ for (i = 0 ; i < 128 ; ++i) if (vs->info[i]) infoDestroy (vs->info[i]) ;
if (vs->nSecondary)
{ for (i = 0 ; i < vs->nSecondary ; ++i) free (vs->secondary[i]) ;
free (vs->secondary) ;
}
free(vs->primary);
OneSchema *t = vs->nxt ;
free (vs) ;
vs = t ;
}
}
/*************************************/
static inline void setCodecBuffer (OneInfo *vi)
{
vi->bufSize = vcMaxSerialSize() + 1; // +1 for added but unused 0-terminator
vi->buffer = new (vi->bufSize, void);
}
static OneFile *oneFileCreate (OneSchema **vsp, char *type)
{ // searches through the linked list of vs to find type, either as primary or a secondary
// if found fills and returns vf, else returns 0
int i, j ;
OneFile *vf = new0 (1, OneFile) ;
char *secondary = 0 ;
OneSchema *vs = *vsp ;
// fprintf (stderr, "oneFileCreate vs %lx type %s\n", (unsigned long)vs, type) ;
// transfer header info
for (i = 0 ; i < 128 ; ++i)
if (vs->info[i]) vf->info[i] = infoDeepCopy (vs->info[i]) ;
// find type in schema
while ((vs = vs->nxt))
if (!strcmp (type, vs->primary))
break ;
else if (vs->nSecondary)
{ for (j = 0 ; j < vs->nSecondary ; ++j)
if (!strcmp (type, vs->secondary[j])) break ;
if (j < vs->nSecondary) { secondary = vs->secondary[j] ; break ; }
}
if (!vs)
{ oneFileDestroy (vf) ;
return 0 ; // failed to find a match
}
// transfer info from matched schema
for (i = 0 ; i < 128 ; ++i)
if (vs->info[i]) vf->info[i] = infoDeepCopy (vs->info[i]) ;
// build binaryTypeUnpack[]
for (i = 0 ; i < 128 ; ++i)
if (vf->info[i] && vf->info[i]->binaryTypePack)
{ U8 x = vf->info[i]->binaryTypePack ;
vf->binaryTypeUnpack[x] = i ;
vf->binaryTypeUnpack[x+1] = i ;
}
// set other information
vf->objectType = vs->objectType ;
vf->groupType = vs->groupType ;
vf->fileType = new (strlen(vs->primary)+1, char);
strcpy (vf->fileType, vs->primary) ;
if (secondary)
{ vf->subType = new (strlen(secondary)+1, char);
strcpy (vf->subType, secondary) ;
}
vf->nFieldMax = vs->nFieldMax ;
vf->field = new (vf->nFieldMax, OneField) ;
// setup for compression
vf->codecTrainingSize = 100000;
setCodecBuffer (vf->info[';']) ;
// determine endian of machine
{ int t = 1;
char *b = (char *) (&t);
vf->isBig = (*b == 0);
}
*vsp = vs ;
return vf ;
}
static void provRefDefCleanup (OneFile *vf)
{ int n ;
if (vf->provenance)
{ OneProvenance *p = vf->provenance ;
for (n = vf->info['!']->accum.count ; n-- ; p++)
{ free (p->program) ;
free (p->version) ;
free (p->command) ;
free (p->date) ;
}
free (vf->provenance) ;
}
if (vf->reference)
{ OneReference *r = vf->reference ;
for (n = vf->info['<']->accum.count ; n-- ; r++)
free (r->filename) ;
free (vf->reference) ;
}
if (vf->deferred)
{ OneReference *r = vf->deferred ;
for (n = vf->info['>']->accum.count ; n-- ; r++)
free (r->filename) ;
free (vf->deferred) ;
}
}
static void oneFileDestroy (OneFile *vf)
{ int i, j;
OneInfo *li, *lx;
if (vf->share)
{ for (i = 0; i < 128 ; i++)
{ lx = vf->info[i];
if (lx != NULL)
{ for (j = 1; j < vf->share; j++)
{ li = vf[j].info[i];
if (li != lx) // the index OneInfos are shared
{ if (li->listCodec == lx->listCodec) li->listCodec = NULL;
infoDestroy(li);
}
}
}
}
for (j = 1; j < vf->share; j++)
{ provRefDefCleanup (&vf[j]) ;
if (vf[j].codecBuf != NULL) free (vf[j].codecBuf);
if (vf[j].f != NULL) fclose (vf[j].f);
}
}
provRefDefCleanup (vf) ;
if (vf->codecBuf != NULL) free (vf->codecBuf);
if (vf->f != NULL && vf->f != stdout) fclose (vf->f);
for (i = 0; i < 128 ; i++)
if (vf->info[i] != NULL)
infoDestroy (vf->info[i]);
if (vf->field) free (vf->field) ;
if (vf->headerText)
{ OneHeaderText *t = vf->headerText ;
while (t)
{ free (t->text) ;
{ OneHeaderText *nxt = t->nxt ; free (t) ; t = nxt ; }
}
}
free(vf->fileType);
free(vf->subType);
free (vf) ;
}
/***********************************************************************************
*
* ASCII PARSING UTILITIES: error reporting, lexical level
*
**********************************************************************************/
void parseError (OneFile *vf, char *format, ...)
{ va_list args;
fprintf (stderr, "ONE PARSE ERROR ");
va_start (args, format);
vfprintf (stderr, format, args);
va_end (args);
vf->lineBuf[vf->linePos] = '\0';
fprintf (stderr, ", line %" PRId64 ": %s\n", vf->line, vf->lineBuf);
exit (1);
}
static inline char vfGetc(OneFile *vf)
{ char c = getc(vf->f);
if (vf->linePos < 127)
vf->lineBuf[vf->linePos++] = c;
return c;
}
static inline void eatWhite (OneFile *vf)
{ char x = vfGetc(vf);
if (x == ' ') // 200414: removed option to have tab instead of space
return;
parseError (vf, "failed to find expected space separation character");
}
static inline char readChar(OneFile *vf)
{ eatWhite(vf);
return vfGetc(vf);
}
static inline char *readBuf(OneFile *vf)
{ char x, *cp, *endBuf;
eatWhite (vf);
endBuf = vf->numberBuf + 32;
for (cp = vf->numberBuf; cp < endBuf ; cp++)
{ x = vfGetc(vf);
if (isspace(x) || x == '\0' || x == EOF)
break;
*cp = x;
}
if (cp >= endBuf)
{ cp[-1] = 0;
parseError (vf, "overlong item %s", vf->numberBuf);
}
else
{ ungetc (x, vf->f);
vf->linePos -= 1;
*cp = 0;
}
return vf->numberBuf;
}
static inline I64 readInt(OneFile *vf)
{ char *e, *b;
I64 x;
b = readBuf(vf);
x = strtoll(b, &e, 10);
if (e == b)
parseError (vf, "empty int field");
if (*e != '\0')
parseError (vf, "bad int");
return x;
}
static inline double readReal(OneFile *vf)
{ char *e, *b;
double x;
b = readBuf(vf);
x = strtod (b, &e);
if (e == b)
parseError (vf, "empty real field");
if (*e != '\0')
parseError (vf, "bad real");
return (x);
}
static inline void readString(OneFile *vf, char *buf, I64 n)
{ eatWhite (vf);
if (vf->isCheckString)
{ char *cp = buf;
--cp;
while (n-- && (*++cp = vfGetc (vf)))
if (*cp == '\n' || *cp == EOF)
break;
if (++n)
parseError (vf, "line too short %d", buf);
*++cp = 0;
}
else
{ if ((I64) fread (buf, 1, n, vf->f) != n)
die ("ONE parse error: failed to read %d byte string", n);
buf[n] = 0 ;
}
}
static inline void readFlush (OneFile *vf) // reads to the end of the line and stores as comment
{ char x;
int n = 0;
OneInfo *li = vf->info['/'] ;
// check the first character - if it is newline then done
x = getc (vf->f) ;
if (x == '\n')
return ;
else if (x != ' ')
parseError (vf, "comment not separated by a space") ;
// else the remainder of the line is a comment
if (!li->bufSize)
{ li->bufSize = 1024 ;
li->buffer = new (li->bufSize, char) ;
}
while ((x = getc (vf->f)) && x != '\n')
if (x == EOF)
parseError (vf, "premature end of file");
else
{ if ((n+1) >= li->bufSize)
{ char *s = new (2*li->bufSize, char) ;
memcpy (s, li->buffer, li->bufSize) ;
free (li->buffer) ;
li->buffer = s ;
li->bufSize *= 2 ;
}
((char*)li->buffer)[n] = x ;
++n ;
}
((char*)li->buffer)[n] = 0 ; // string terminator
}
/***********************************************************************************
*
* LIST BUFFER & COUNT MANAGEMENT: error reporting, lexical level
*
**********************************************************************************/
// Ensure line type t buffer can handles size+nStrings, and accumulate counts
static inline void updateCountsAndBuffer (OneFile *vf, char t, I64 size, I64 nStrings)
{ OneInfo *li;
li = vf->info[(int) t];
li->accum.total += size;
if (size > li->accum.max)
li->accum.max = size;
size += nStrings; // need to allocate space for terminal 0s
if ( ! li->isUserBuf && size > li->bufSize) // expand buffer
{ if (li->buffer != NULL) free (li->buffer);
li->bufSize = size;
li->buffer = new (size*li->listEltSize, void);
}
}
// Called when a new group starts or eof, accumulate group counts since last group start
static inline void updateGroupCount(OneFile *vf, bool isGroupLine)
{ int i;
OneInfo *li;
OneCounts *ci;
for (i = 'A'; i <= 'Z' ; i++)
{ li = vf->info[i];
if (li != NULL)
{ ci = &(li->accum);
if (vf->inGroup)
{ if (ci->groupCount < ci->count - li->gCount)
ci->groupCount = ci->count - li->gCount;
if (ci->groupTotal < ci->total - li->gTotal)
ci->groupTotal = ci->total - li->gTotal;
}
else
{ li->oCount = ci->count;
li->oTotal = ci->total;
}
li->gCount = ci->count;
li->gTotal = ci->total;
}
}
if (isGroupLine)
{ vf->group += 1;
vf->inGroup = true;
}
}
/***********************************************************************************
*
* BINARY INT LIST COMPACTION & UNCOMPACTION
*
**********************************************************************************/
static char *compactIntList (OneFile *vf, OneInfo *li, I64 len, char *buf, int *usedBytes)
{ char *y;
int d, k;
I64 z, i, mask, *ibuf;
ibuf = (I64 *) buf;
for (i = len-1; i > 0; i--) // convert to differences - often a big win, else harmless
ibuf[i] -= ibuf[i-1];
mask = 0; // find how many top bytes can be skipped
for (i = 1; i < len; i++)
if (ibuf[i] >= 0)
mask |= ibuf[i];
else
mask |= -(ibuf[i]+1);
k = sizeof(I64) ;
mask >>= 7;
for (d = 1; d < k; d++)
{ if (mask == 0)
break;
mask >>= 8;
}
*usedBytes = d ;
z = k - d; // number of 0 bytes
if (z == 0) return (char*)&ibuf[1] ;
if (buf != li->buffer && !li->isUserBuf && (I64) (li->bufSize*sizeof(I64)) < d*len)
{ if (li->buffer != NULL)
free (li->buffer);
li->bufSize = ((d*len) / sizeof(I64)) + 1;
li->buffer = new (li->bufSize * sizeof(I64), void);
}
y = li->buffer ;
buf += sizeof(I64) ; --len ; // don't record the first element of buf, which is not a diff
if (vf->isBig) // copy d bytes per I64, ignoring z before or after depending on isBig
while (len--)
{ buf += z;
for (k = 0; k < d; k++)
*y++ = *buf++;
}
else
while (len--)
{ for (k = 0; k < d; k++)
*y++ = *buf++;
buf += z;
}
return li->buffer ;
}
static void decompactIntList (OneFile *vf, I64 len, char *buf, int usedBytes)
{ int d, z, k;
char *s, *t;
z = sizeof(I64) - usedBytes ;
if (z > 0) // decompacts in place
{ buf += sizeof(I64) ; --len ; // don't decompact 0th element
d = usedBytes;
s = buf + d*len;
t = s + z*len;
if (vf->isBig)
while (s > buf)
{ for (k = 0; k < d; k++)
*--t = *--s;
if (*s & 0x80)
for (k = 0; k < z; k++)
*--t = 0xff;
else
for (k = 0; k < z; k++)
*--t = 0x0;
}
else
while (s > buf)
{ if (s[-1] & 0x80)
for (k = 0; k < z; k++)
*--t = 0xff;
else
for (k = 0; k < z; k++)
*--t = 0;
for (k = 0; k < d; k++)
*--t = *--s;
}
buf -= sizeof(I64) ; ++len ;
}
{ I64 i, *x = (I64 *) buf; // revert differencing
for (i = 1; i < len; i++)
x[i] += x[i-1];
}
}
// read and write compressed fields
static inline int writeCompressedFields (FILE *f, OneField *field, OneInfo *li)
{
int i, n = 0 ;
for (i = 0 ; i < li->nField ; ++i)
switch (li->fieldType[i])
{
case oneREAL: fwrite (&field[i].r, 8, 1, f) ; n += 8 ; break ;
case oneCHAR: putc (field[i].c, f) ; ++n ; break ;
default: // includes INT and all the LISTs, which store their length in field as an INT
n += ltfWrite (field[i].i, f) ;
}
return n ;
}
static inline void readCompressedFields (FILE *f, OneField *field, OneInfo *li)
{
int i ;
for (i = 0 ; i < li->nField ; ++i)
switch (li->fieldType[i])
{
case oneREAL: fread (&field[i].r, 8, 1, f) ; break ;
case oneCHAR: field[i].c = fgetc (f) ; break ;
default: // includes INT and all the LISTs, which store their length in field as an INT
field[i].i = ltfRead (f) ;
}
}
/***********************************************************************************
*
* ONE_READ_LINE:
* Reads the next line and returns false at end of file or on error. The line is
* parsed according to its linetype and contents accessed by macros that follow.
* The top bit of the first character determines whether the line is binary or ascii
*
**********************************************************************************/
// Read a string list, first into new allocs, then into sized line buffer.
// Annoyingly inefficient, but we don't use it very much.
static void readStringList(OneFile *vf, char t, I64 len)
{ int j;
I64 totLen, sLen;
char **string, *buf;
totLen = 0;
string = new (len, char *);
for (j = 0; j < len ; ++j)
{ sLen = readInt (vf);
totLen += sLen;
string[j] = new (sLen+1, char);
readString (vf, string[j], sLen);
}
updateCountsAndBuffer (vf, t, totLen, len);
buf = (char *) vf->info[(int) t]->buffer;
for (j = 0; j < len ; ++j)
{ strcpy (buf, string[j]);
buf += strlen(buf) + 1;
free (string[j]);
}
free (string);
}
static bool addProvenance(OneFile *vf, OneProvenance *from, int n) ; // need forward declaration
char oneReadLine (OneFile *vf)
{ bool isAscii;
U8 x;
char t;
OneInfo *li;
assert (!vf->isWrite) ;
assert (!vf->isFinal) ;
vf->linePos = 0; // must come before first vfGetc()
x = vfGetc (vf); // read first char
if (feof (vf->f) || x == '\n') // blank line (x=='\n') is end of records marker before footer
{ vf->lineType = 0 ; // additional marker of end of file
return 0;
}
vf->line += 1; // otherwise assume this is a good line, and die if not
if (x & 0x80)
{ isAscii = false;
t = vf->binaryTypeUnpack[x];
}
else
{ isAscii = true;
t = x;
}
vf->lineType = t;
li = vf->info[(int) t];
if (li == NULL)
parseError (vf, "unknown line type %c(%d was %d) line %d", t, t, x, (int)vf->line);
li->accum.count += 1;
if (t == vf->objectType)
vf->object += 1;
if (t == vf->groupType)
updateGroupCount (vf, true);
// fprintf (stderr, "reading line %" PRId64 " type %c nField %d listElt %d\n", vf->line, t, li->nField, li->listEltSize) ;
if (vf->info['/']->bufSize) // clear the comment buffer
*(char*)(vf->info['/']->buffer) = 0 ;
vf->nBits = 0 ; // will use for any compressed data read in
if (isAscii) // read field by field according to ascii spec
{ int i, j;
I64 *ilst, len;
double *rlst;
for (i = 0; i < li->nField; i++)
switch (li->fieldType[i])
{
case oneINT:
vf->field[i].i = readInt (vf);
// printf (" field %d int %d\n", i, (int)oneInt(vf,i)) ;
break;
case oneREAL:
vf->field[i].r = readReal (vf);
break;
case oneCHAR:
vf->field[i].c = readChar (vf);
// printf (" field %d char %c\n", i, (int)oneChar(vf,i)) ;
break;
case oneSTRING:
case oneDNA: