void processFrameFiles(char *tabFile, int numFramesFiles, char **framesFiles)
/* combine and sort input files, adding bin column and write top tabFile */
{
/* sort by chrom location, accounting for bin column */
static char *cmd[] = {"sort", "-k", "2,2", "-k", "3,3n", NULL};
int i;
struct pipeline *pl = pipelineOpen1(cmd, pipelineWrite, tabFile, NULL);
FILE *sortFh = pipelineFile(pl);
for (i = 0; i < numFramesFiles; i++)
processFrameFile(sortFh, framesFiles[i]);
pipelineWait(pl);
}
struct pipeline *textOutInit(char *fileName, char *compressType)
/* Set up stdout to be HTTP text, file (if fileName is specified), or
* compressed file (if both fileName and compressType are specified --
* see textOut.h for supported compression types).
* Return NULL if no compression, otherwise a pipeline handle on which
* textOutClose should be called when we're done writing stdout. */
{
struct pipeline *compressPipeline = NULL;
trimSpaces(fileName);
if (isEmpty(fileName))
{
printf("Content-Type: text/plain\n\n");
}
else if (isEmpty(compressType) || sameWord(compressType, textOutCompressNone))
{
printf("Content-Type: application/octet-stream\n");
printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
}
else
{
char *suffix = getCompressSuffix(compressType);
printf("Content-Type: application/x-%s\n", compressType);
if (endsWith(fileName, suffix))
printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
else
printf("Content-Disposition: attachment; filename=%s%s\n\n",
fileName, suffix);
/* Send the Content header uncompressed! */
fflush(stdout);
/* Make sure no environment variables interfere with compressor. */
cleanEnvVars(compressType);
/* Redirect stdout to compressor pipeline object. */
compressPipeline = pipelineOpen1(getCompressor(compressType),
pipelineWrite, NULL, NULL);
if (-1 == dup2(pipelineFd(compressPipeline), STDOUT_FILENO))
errnoAbort("dup2(pipelineFd %d, stdout %d) failed in textOpen()",
pipelineFd(compressPipeline), STDOUT_FILENO);
}
pushWarnHandler(textOutWarnHandler);
pushAbortHandler(textOutAbortHandler);
return(compressPipeline);
}
struct lineFile *lineFileDecompress(char *fileName, bool zTerm)
/* open a linefile with decompression */
{
struct pipeline *pl;
struct lineFile *lf;
char *testName = NULL;
char *testbytes = NULL; /* the header signatures for .gz, .bz2, .Z,
* .zip are all 2-4 bytes only */
if (fileName==NULL)
return NULL;
testbytes=headerBytes(fileName,4);
if (!testbytes)
return NULL; /* avoid error from pipeline */
testName=getFileNameFromHdrSig(testbytes);
freez(&testbytes);
if (!testName)
return NULL; /* avoid error from pipeline */
pl = pipelineOpen1(getDecompressor(fileName), pipelineRead, fileName, NULL);
lf = lineFileAttach(fileName, zTerm, pipelineFd(pl));
lf->pl = pl;
return lf;
}
struct pipeline *textOutInit(char *fileName, char *compressType, int *saveStdout)
/* Set up stdout to be HTTP text, file (if fileName is specified), or
* compressed file (if both fileName and compressType are specified --
* see textOut.h for supported compression types).
* Return NULL if no compression, otherwise a pipeline handle on which
* textOutClose should be called when we're done writing stdout. */
{
struct pipeline *compressPipeline = NULL;
// if path contains a slash, we are outputting to a local file
boolean outToFile = (strchr(fileName, '/') != NULL);
if (outToFile)
{
FILE *f;
f = fopen(fileName, "w");
/* We want to capture stdout output to a file */
fflush(stdout);
int tempOut = dup(STDOUT_FILENO);
if (saveStdout)
*saveStdout = tempOut;
dup2(fileno(f),STDOUT_FILENO); /* closes STDOUT before setting it again */
fclose(f);
}
trimSpaces(fileName);
if (isEmpty(fileName))
{
printf("Content-Type: text/plain\n\n");
}
else if (isEmpty(compressType) || sameWord(compressType, textOutCompressNone))
{
if (!outToFile)
{
printf("Content-Type: application/octet-stream\n");
printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
}
}
else
{
if (!outToFile)
{
char *suffix = getCompressSuffix(compressType);
printf("Content-Type: application/x-%s\n", compressType);
if (endsWith(fileName, suffix))
printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
else
printf("Content-Disposition: attachment; filename=%s%s\n\n",
fileName, suffix);
/* Send the Content header uncompressed! */
fflush(stdout);
}
/* Make sure no environment variables interfere with compressor. */
cleanEnvVars(compressType);
/* Redirect stdout to compressor pipeline object. */
compressPipeline = pipelineOpen1(getCompressor(compressType),
pipelineWrite, NULL, NULL);
if (-1 == dup2(pipelineFd(compressPipeline), STDOUT_FILENO))
errnoAbort("dup2(pipelineFd %d, stdout %d) failed in textOpen()",
pipelineFd(compressPipeline), STDOUT_FILENO);
}
pushWarnHandler(textOutWarnHandler);
pushAbortHandler(textOutAbortHandler);
return(compressPipeline);
}
