struct lineFile* gzLineFileOpen(char *fileName)
/* Open a line file, checking the file name to determine if the file is
* compressed. If it ends in .gz, .Z, or .bz2 it will be piped through the
* approriate decompression program. Must use gzLineFileClose() to close the
* file. */
{
char **compressor = gbGetCompressor(fileName, "r");
if (compressor != NULL)
{
char *argv[4], **cmds[2];
struct gbPipeline *pipeline;
argv[0] = compressor[0];
argv[1] = compressor[1];
argv[2] = fileName;
argv[3] = NULL;
cmds[0] = argv;
cmds[1] = NULL;
pipeline = gbPipelineCreate(cmds, PIPELINE_READ, NULL, NULL);
return lineFileAttach(gbPipelineDesc(pipeline),
TRUE, gbPipelineFd(pipeline));
}
else
return lineFileOpen(fileName, TRUE);
}
FILE *openSortOutput(char *fileName, char **sortSpec)
/* Open a pipeline to sort and compress output. SortSpec is null-terminated
* list of fields options to pass to sort. gSortTmpDir maybe null.
* gbOutputRename is used to install and close.
*/
{
struct gbPipeline *pipeline;
char tmpPath[PATH_LEN];
char **compressor;
char **sortCmd, **cmds[3];
int nSort, iSort = 0, i;
/* sort cmd, nSort includes cmd and NULL */
for (nSort = 0; sortSpec[nSort] != NULL; nSort++)
continue;
if (gSortTmp != NULL)
nSort += 2;
nSort += 2; /* for "sort" and NULL */
sortCmd = alloca(nSort*sizeof(char*));
sortCmd[iSort++] = "sort";
if (gSortTmp != NULL)
{
sortCmd[iSort++] = "-T";
sortCmd[iSort++] = gSortTmp;
}
for (i = 0; sortSpec[i] != NULL; i++)
sortCmd[iSort++] = sortSpec[i];
sortCmd[iSort] = NULL;
assert(iSort < nSort);
cmds[0] = sortCmd;
cmds[1] = NULL;
/* compress process, if needed */
compressor = gbGetCompressor(fileName, "w");
if (compressor != NULL)
{
cmds[1] = compressor;
cmds[2] = NULL;
}
/* tmp name to output to */
gbGetOutputTmp(fileName, tmpPath);
gbMakeFileDirs(tmpPath);
pipeline = gbPipelineCreate(cmds, PIPELINE_WRITE|PIPELINE_FDOPEN, NULL,
tmpPath);
return gbPipelineFile(pipeline);
}
FILE* gzMustOpen(char* fileName, char *mode)
/* Open a file for read or write access. If it ends in .gz, .Z, or .bz2 it
* will be piped through the approriate decompression program. Must use
* gzClose() to close the file. */
{
char **compressor = gbGetCompressor(fileName, mode);
if (compressor != NULL)
{
char *argv[4], *outFile, **cmds[2];
unsigned options = PIPELINE_FDOPEN;
struct gbPipeline *pipeline;
argv[0] = compressor[0];
argv[1] = compressor[1];
/* compress options */
if (sameString(mode, "r"))
{
argv[2] = fileName;
argv[3] = NULL;
outFile = NULL;
options |= PIPELINE_READ;
}
else
{
argv[2] = NULL;
outFile = fileName;
if (sameString(mode, "w"))
options |= PIPELINE_WRITE;
else if (sameString(mode, "a"))
errAbort("gzMustOpen append mode does not work for compressed output");
else
errAbort("invalid mode for gzMustOpen \"%s\"", mode);
}
cmds[0] = argv;
cmds[1] = NULL;
pipeline = gbPipelineCreate(cmds, options, NULL, outFile);
return gbPipelineFile(pipeline);
}
else
return mustOpen(fileName, mode);
}
void gbGetOutputTmp(char *path, char *tmpPath)
/* generate the tmp path name, moving the compress extension if needed */
{
char savedExt[32];
int len;
savedExt[0] = '\0';
strcpy(tmpPath, path);
/* don't add extension for special names */
if (!isSpecialName(path))
{
if (gbGetCompressor(tmpPath, "r") != NULL)
{
char *last = strrchr(tmpPath, '.');
strcpy(savedExt, last);
*last = '\0';
}
len = strlen(tmpPath);
safef(tmpPath+len, PATH_LEN-len, ".%d.%s.tmp%s", getpid(), getHost(),
savedExt);
}
}
