84f9843f1c767648dde8a3afafa8762c21b6a0cc
angie
Tue Mar 22 10:57:28 2011 -0700
Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself
to remove the calls to warn, because I want the CGIs to get those
using the webAbort error handlers in conjunction w/errCatch etc.
There are tons of calls to warn() in our lib code, which can be
redirected using the errAbort handler stack if desired.
diff --git src/inc/linefile.h src/inc/linefile.h
index 62ccc3a..e6bbc9b 100644
--- src/inc/linefile.h
+++ src/inc/linefile.h
@@ -1,238 +1,238 @@
/* lineFile - stuff to rapidly read text files and parse them into
* lines.
*
* This file is copyright 2002 Jim Kent, but license is hereby
* granted for all use - public, private or commercial. */
#ifndef LINEFILE_H
#define LINEFILE_H
#ifdef USE_TABIX
#include "tabix.h"
#endif
enum nlType {
nlt_undet, /* undetermined */
nlt_unix, /* lf */
nlt_dos, /* crlf */
nlt_mac /* cr */
};
struct metaOutput
/* struct to store list of file handles to output meta data to
* meta data is text after # */
{
struct metaOutput *next; /* next file handle */
FILE *metaFile; /* file to write metadata to */
};
struct lineFile
/* Structure to handle fast, line oriented
* fileIo. */
{
struct lineFile *next; /* Might need to be on a list. */
char *fileName; /* Name of file. */
int fd; /* File handle. -1 for 'memory' files. */
int bufSize; /* Size of buffer. */
off_t bufOffsetInFile; /* Offset in file of first buffer byte. */
int bytesInBuf; /* Bytes read into buffer. */
int reserved; /* Reserved (zero for now). */
int lineIx; /* Current line. */
int lineStart; /* Offset of line in buffer. */
int lineEnd; /* End of line in buffer. */
bool zTerm; /* Replace '\n' with zero? */
enum nlType nlType; /* type of line endings: dos, unix, mac or undet */
bool reuse; /* Set if reusing input. */
char *buf; /* Buffer. */
struct pipeline *pl; /* pipeline if reading compressed */
struct metaOutput *metaOutput; /* list of FILE handles to write metaData to */
bool isMetaUnique; /* if set, do not repeat comments in output */
struct hash *metaLines; /* save lines to suppress repetition */
#ifdef USE_TABIX
tabix_t *tabix; /* A tabix-compressed file and its binary index file (.tbi) */
ti_iter_t tabixIter; /* An iterator to get decompressed indexed lines of text */
#endif
};
char *getFileNameFromHdrSig(char *m);
/* Check if header has signature of supported compression stream,
and return a phoney filename for it, or NULL if no sig found. */
struct lineFile *lineFileDecompressFd(char *name, bool zTerm, int fd);
/* open a linefile with decompression from a file or socket descriptor */
struct lineFile *lineFileDecompressMem(bool zTerm, char *mem, long size);
/* open a linefile with decompression from a memory stream */
struct lineFile *lineFileMayOpen(char *fileName, bool zTerm);
/* Try and open up a lineFile. If fileName ends in .gz, .Z, or .bz2,
* it will be read from a decompress pipeline. */
struct lineFile *lineFileOpen(char *fileName, bool zTerm);
/* Open up a lineFile or die trying If fileName ends in .gz, .Z, or .bz2,
* it will be read from a decompress pipeline.. */
struct lineFile *lineFileAttach(char *fileName, bool zTerm, int fd);
/* Wrap a line file around an open'd file. */
struct lineFile *lineFileStdin(bool zTerm);
/* Wrap a line file around stdin. */
struct lineFile *lineFileOnString(char *name, bool zTerm, char *s);
/* Wrap a line file object around string in memory. This buffer
* have zeroes written into it if zTerm is non-zero. It will
* be freed when the line file is closed. */
void lineFileClose(struct lineFile **pLf);
/* Close up a line file. */
void lineFileCloseList(struct lineFile **pList);
/* Close up a list of line files. */
boolean lineFileNext(struct lineFile *lf, char **retStart, int *retSize);
/* Fetch next line from file. */
boolean lineFileNextReal(struct lineFile *lf, char **retStart);
/* Fetch next line from file that is not blank and
* does not start with a '#'. */
void lineFileNeedNext(struct lineFile *lf, char **retStart, int *retSize);
/* Fetch next line from file. Squawk and die if it's not there. */
void lineFileReuse(struct lineFile *lf);
/* Reuse current line. */
#define lineFileString(lf) ((lf)->buf + (lf)->lineStart)
/* Current string in line file. */
#define lineFileTell(lf) ((lf)->bufOffsetInFile + (lf)->lineStart)
/* Current offset (of string start) in file. */
void lineFileSeek(struct lineFile *lf, off_t offset, int whence);
/* Seek to read next line from given position. */
void lineFileRewind(struct lineFile *lf);
/* Return lineFile to start. */
void lineFileAbort(struct lineFile *lf, char *format, ...)
/* Print file name, line number, and error message, and abort. */
#if defined(__GNUC__)
__attribute__((format(printf, 2, 3)))
#endif
;
void lineFileVaAbort(struct lineFile *lf, char *format, va_list args);
/* Print file name, line number, and error message, and abort. */
void lineFileUnexpectedEnd(struct lineFile *lf);
/* Complain about unexpected end of file. */
void lineFileExpectWords(struct lineFile *lf, int expecting, int got);
/* Check line has right number of words. */
void lineFileExpectAtLeast(struct lineFile *lf, int expecting, int got);
/* Check line has right number of words. */
void lineFileShort(struct lineFile *lf);
/* Complain that line is too short. */
boolean lineFileNextRow(struct lineFile *lf, char *words[], int wordCount);
/* Return next non-blank line that doesn't start with '#' chopped into words.
* Returns FALSE at EOF. Aborts on error. */
#define lineFileRow(lf, words) lineFileNextRow(lf, words, ArraySize(words))
/* Read in line chopped into fixed size word array. */
boolean lineFileNextCharRow(struct lineFile *lf, char sep, char *words[], int wordCount);
/* Return next non-blank line that doesn't start with '#' chopped into words
* delimited by sep. Returns FALSE at EOF. Aborts on error. */
boolean lineFileNextRowTab(struct lineFile *lf, char *words[], int wordCount);
/* Return next non-blank line that doesn't start with '#' chopped into words
* at tabs. Returns FALSE at EOF. Aborts on error. */
#define lineFileRowTab(lf, words) \
lineFileNextRowTab(lf, words, ArraySize(words))
/* Read in line chopped by tab into fixed size word array. */
int lineFileChopNext(struct lineFile *lf, char *words[], int maxWords);
/* Return next non-blank line that doesn't start with '#' chopped into words. */
#define lineFileChop(lf, words) lineFileChopNext(lf, words, ArraySize(words))
/* Ease-of-usef macro for lineFileChopNext above. */
int lineFileChopCharNext(struct lineFile *lf, char sep, char *words[], int maxWords);
/* Return next non-blank line that doesn't start with '#' chopped into
words delimited by sep. */
int lineFileChopNextTab(struct lineFile *lf, char *words[], int maxWords);
/* Return next non-blank line that doesn't start with '#' chopped into words
* on tabs */
#define lineFileChopTab(lf, words) lineFileChopNextTab(lf, words, ArraySize(words))
/* Ease-of-usef macro for lineFileChopNext above. */
int lineFileNeedNum(struct lineFile *lf, char *words[], int wordIx);
/* Make sure that words[wordIx] is an ascii integer, and return
* binary representation of it. */
int lineFileNeedFullNum(struct lineFile *lf, char *words[], int wordIx);
/* Make sure that words[wordIx] is an ascii integer, and return
* binary representation of it. Require all chars in word to be digits.*/
double lineFileNeedDouble(struct lineFile *lf, char *words[], int wordIx);
/* Make sure that words[wordIx] is an ascii double value, and return
* binary representation of it. */
void lineFileSkip(struct lineFile *lf, int lineCount);
/* Skip a number of lines. */
char *lineFileSkipToLineStartingWith(struct lineFile *lf, char *start, int maxCount);
/* Skip to next line that starts with given string. Return NULL
* if no such line found, otherwise return the line. */
char *lineFileReadAll(struct lineFile *lf);
/* Read remainder of lineFile and return it as a string. */
boolean lineFileParseHttpHeader(struct lineFile *lf, char **hdr,
boolean *chunked, int *contentLength);
/* Extract HTTP response header from lf into hdr, tell if it's
* "Transfer-Encoding: chunked" or if it has a contentLength. */
struct dyString *lineFileSlurpHttpBody(struct lineFile *lf,
boolean chunked, int contentLength);
/* Return a dyString that contains the http response body in lf. Handle
* chunk-encoding and content-length. */
void lineFileSetMetaDataOutput(struct lineFile *lf, FILE *f);
/* set file to write meta data to,
* should be called before reading from input file */
void lineFileSetUniqueMetaData(struct lineFile *lf);
/* suppress duplicate lines in metadata */
void lineFileRemoveInitialCustomTrackLines(struct lineFile *lf);
/* remove initial browser and track lines */
/*----- Optionally-compiled wrapper on tabix (compression + indexing): -----*/
#define COMPILE_WITH_TABIX "%s: Sorry, this functionality is available only when\n" \
"you have installed the tabix library from\n" \
"http://samtools.sourceforge.net/ and rebuilt kent/src with USE_TABIX=1\n" \
"(see http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables)."
-struct lineFile *lineFileOnTabix(char *fileOrUrl, bool zTerm);
+struct lineFile *lineFileTabixMayOpen(char *fileOrUrl, bool zTerm);
/* Wrap a line file around a data file that has been compressed and indexed
* by the tabix command line program. The index file <fileName>.tbi must be
* readable in addition to fileName. If there's a problem, warn & return NULL.
* This works only if kent/src has been compiled with USE_TABIX=1 and linked
* with the tabix C library. */
boolean lineFileSetTabixRegion(struct lineFile *lf, char *seqName, int start, int end);
-/* Assuming lf was created by lineFileOnTabix, tell tabix to seek to the specified region
+/* Assuming lf was created by lineFileTabixMayOpen, tell tabix to seek to the specified region
* and return TRUE (or if there are no items in region, return FALSE). */
#endif /* LINEFILE_H */