boolean bamFileExists(char *fileOrUrl)
/* Return TRUE if we can successfully open the bam file and its index file. */
{
char *bamFileName = fileOrUrl;
samfile_t *fh = samopen(bamFileName, "rb", NULL);
boolean usingUrl = TRUE;
usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
if (fh != NULL)
{
#ifndef KNETFILE_HOOKS
// When file is an URL, this caches the index file in addition to validating:
// Since samtools's url-handling code saves the .bai file to the current directory,
// chdir to a trash directory before calling bam_index_load, then chdir back.
char *runDir = getCurrentDir();
char *samDir = getSamDir();
if (usingUrl)
setCurrentDir(samDir);
#endif//ndef KNETFILE_HOOKS
bam_index_t *idx = bam_index_load(bamFileName);
#ifndef KNETFILE_HOOKS
if (usingUrl)
setCurrentDir(runDir);
#endif//ndef KNETFILE_HOOKS
samclose(fh);
if (idx == NULL)
{
warn("bamFileExists: failed to read index corresponding to %s", bamFileName);
return FALSE;
}
free(idx); // Not freeMem, freez etc -- sam just uses malloc/calloc.
return TRUE;
}
return FALSE;
}
/**
* Reads the layout info stored in the given (XML) file and creates figure templates.
* Existing templates remain in where they are but are replaced if a new definition with an existing name is found.
*
* @param filename The name of the file to load.
* @return Returns GC_NO_ERROR if everything was ok, otherwise an error code.
*/
TGCError CGenericCanvas::addLayoutsFromFile(const char* filename)
{
TGCError result = GC_NO_ERROR;
xmlNodePtr root, current;
CFigureParser parser(this);
parser.addListener(&FListener);
string currentDir = getCurrentDir();
xmlDocPtr document = xmlParseFile(utf8ToANSI(string(filename)).c_str());
if (document == NULL)
return GC_XML_PARSE_ERROR;
root = xmlDocGetRootElement(document);
if (root == NULL)
{
xmlFreeDoc(document);
error(this, "XML Error: Template file is empty.");
return GC_XML_EMPTY_DOCUMENT;
}
if (!XML_IS(root, "gc-layouts"))
{
xmlFreeDoc(document);
error(this, "XML Error: Template file invalid.");
return GC_XML_INVALID_DOCUMENT;
}
// Switch to the directory of the given file. This is necessary to make relative file names working.
string path = extractFilePath(filename);
setCurrentDir(path);
// Parse description elements.
glMatrixMode(GL_MODELVIEW);
current = root->children;
while (current != NULL)
{
// Be flexible, ignore any unknown layout entries.
if (XML_IS(current, "layout-definition"))
parser.parseLayoutDefinition(current, FModel);
else
if (XML_IS(current, "connection-definition"))
parser.parseDecorDefinition(current, FModel);
current = current->next;
}
setCurrentDir(currentDir);
xmlFreeDoc(document);
parser.removeListener(&FListener);
return result;
}
struct fileInfo *listDirX(char *dir, char *pattern, boolean fullPath)
/* Return list of files matching wildcard pattern with
* extra info. If full path is true then the path will be
* included in the name of each file. */
{
struct fileInfo *list = NULL, *el;
long hFile;
struct _finddata_t fileInfo;
boolean otherDir = FALSE;
char *currentDir;
int dirNameSize = strlen(dir);
int fileNameOffset = dirNameSize+1;
char pathName[512];
if (dir == NULL || sameString(".", dir) || sameString("", dir))
dir = "";
else
{
currentDir = getCurrentDir();
setCurrentDir(dir);
otherDir = TRUE;
}
if (pattern == NULL)
pattern = "*";
if( (hFile = _findfirst( pattern, &fileInfo)) == -1L )
return NULL;
memcpy(pathName, dir, dirNameSize);
pathName[dirNameSize] = '/';
do
{
if (!sameString(".", fileInfo.name) && !sameString("..", fileInfo.name))
{
char *fileName = fileInfo.name;
strcpy(pathName+fileNameOffset, fileName);
if (fullPath)
fileName = pathName;
el = newFileInfo(fileInfo.name, fileInfo.size,
fileInfo.attrib & _A_SUBDIR, 0,
fileInfo.time_access);
slAddHead(&list, el);
}
}
while( _findnext( hFile, &fileInfo) == 0 );
_findclose( hFile );
if (otherDir)
setCurrentDir(currentDir);
slSort(&list, cmpFileInfo);
return list;
}
int main(int argc, char *argv[])
{
optionInit(&argc, argv, options);
if (argc != 9)
usage("wrong number of args");
if (optionExists("-help"))
usage("help");
startTag = argv[1];
endTag = argv[2];
startDate = argv[3];
endDate = argv[4];
title = argv[5];
repoDir = argv[6];
outDir = argv[7];
outPrefix = argv[8];
contextSize = optionInt("-context", 15);
userHash = hashNew(5);
setCurrentDir(repoDir);
gitReports();
hashFree(&userHash);
printf("Done.\n");
return 0;
}
// --------------------------------------------------------------------------------------------------------
void KFileTreeWidget::refresh ()
{
if (current_dir_node) // redisplay the current directory
{
std::string currentDirPath = current_dir_node->getAbsPathName();
removeAllPickables();
delete current_dir_node;
current_dir_node = NULL;
setCurrentDir(currentDirPath);
}
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
char *workDir = optionVal("workDir", CGI_BIN);
setCurrentDir(workDir);
refreshNamedSessionCustomTracks(argv[1]);
return 0;
}
struct slName *listDir(char *dir, char *pattern)
/* Return an alphabetized list of all files that match
* the wildcard pattern in directory. */
{
long hFile;
struct _finddata_t fileInfo;
struct slName *list = NULL, *name;
boolean otherDir = FALSE;
char *currentDir;
if (dir == NULL || sameString(".", dir) || sameString("", dir))
dir = "";
else
{
currentDir = getCurrentDir();
setCurrentDir(dir);
otherDir = TRUE;
}
if (pattern == NULL)
pattern = *;
if( (hFile = _findfirst( pattern, &fileInfo)) == -1L )
return NULL;
do
{
if (!sameString(".", fileInfo.name) && !sameString("..", fileInfo.name))
{
name = newSlName(fileInfo.name);
slAddHead(&list, name);
}
}
while( _findnext( hFile, &fileInfo) == 0 );
_findclose( hFile );
if (otherDir)
setCurrentDir(currentDir);
slNameSort(&list);
return list;
}
// --------------------------------------------------------------------------------------------------------
void KFileTreeWidget::doubleClicked ()
{
if (picked_pickable == current_dir_node) return;
if (((KFileTreeNode*)picked_pickable)->getType() == KDL_FILE_TYPE_DIR)
{
setCurrentDir (((KFileTreeNode*)picked_pickable)->getAbsPathName());
}
else
{
notifyReceivers (((KFileTreeNode*)picked_pickable)->getAbsPathName(), KDL_NOTIFICATION_TYPE_OPEN_FILE);
notifyReceivers ();
}
}
void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
samfile_t **pSamFile)
/* Open the .bam file, fetch items in the seq:start-end position range,
* and call callbackFunc on each bam item retrieved from the file plus callbackData.
* This handles BAM files with "chr"-less sequence names, e.g. from Ensembl.
* The pSamFile parameter is optional. If non-NULL it will be filled in, just for
* the benefit of the callback function, with the open samFile. */
{
char *bamFileName = NULL;
samfile_t *fh = bamOpen(fileOrUrl, &bamFileName);
boolean usingUrl = TRUE;
usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
if (pSamFile != NULL)
*pSamFile = fh;
#ifndef KNETFILE_HOOKS
// Since samtools' url-handling code saves the .bai file to the current directory,
// chdir to a trash directory before calling bam_index_load, then chdir back.
char *runDir = getCurrentDir();
char *samDir = getSamDir();
if (usingUrl)
setCurrentDir(samDir);
#endif//ndef KNETFILE_HOOKS
bam_index_t *idx = bam_index_load(bamFileName);
#ifndef KNETFILE_HOOKS
if (usingUrl)
setCurrentDir(runDir);
#endif//ndef KNETFILE_HOOKS
if (idx == NULL)
warn("bam_index_load(%s) failed.", bamFileName);
else
{
bamFetchAlreadyOpen(fh, idx, bamFileName, position, callbackFunc, callbackData);
free(idx); // Not freeMem, freez etc -- sam just uses malloc/calloc.
}
bamClose(&fh);
}
void newProg(char *module, char *description)
/* newProg - make a new C source skeleton. */
{
char fileName[512];
char dirName[512];
char fileOnly[128];
safef(dirName, sizeof(dirName), "%s", module);
makeDir(dirName);
splitPath(dirName, NULL, fileOnly, NULL);
safef(fileName, sizeof(fileName), "%s/%s.c", dirName, fileOnly);
makeC(fileOnly, description, fileName);
/* makefile is now constructed properly with ../.. paths */
setCurrentDir(dirName);
makeMakefile(fileOnly, "makefile");
}
// --------------------------------------------------------------------------------------------------------
void KFileTreeWidget::menuCallback ( const std::string & itemText )
{
if (itemText == "show more")
{
KFileTreeDir::max_path_depth++;
refresh();
return;
}
else if (itemText == "show less")
{
if (KFileTreeDir::max_path_depth <= 1) return;
KFileTreeDir::max_path_depth--;
refresh();
return;
}
KFileTreeDir * dir;
if (picked_pickable)
{
if (((KFileTreeNode*)picked_pickable)->getType() == KDL_FILE_TYPE_DIR)
{
dir = (KFileTreeDir*)picked_pickable;
if (itemText == "cd")
{
if (dir != current_dir_node)
{
setCurrentDir(dir->getAbsPathName());
}
return;
}
else if (itemText == "show texture(s)")
{
}
}
else
{
if (itemText == "show texture(s)")
{
}
}
}
}
void wigTestMaker(char *outDir)
/* wigTestMaker - Create test wig files.. */
{
makeDir(outDir);
setCurrentDir(outDir);
makeChromSizes("chrom.sizes", 100);
makeEmpty("empty.wig");
makeEmptyFixed("emptyFixed.wig");
makeEmptyVar("emptyVar.wig");
makeShortFixed("shortFixed.wig");
makeShortVar("shortVar.wig");
makeShortBed("shortBed.wig");
makeSineSineFixed("sineSineFixed.wig", 1000, 500, 10, 8);
makeSineSineVar("sineSineVar.wig", 1000, 500, 10, 4);
makeSineSineBed("sineSineBed.wig", 1000, 500, 10, 2);
makeIncreasing("increasing.wig");
makeMixem("mixem.wig");
makeContigSizes("contig.sizes", 666666);
makeManyContigs("contigs.wig", 666666);
}
fs_node_t *initialise_initrd(u32int location)
{
fs_location = kmalloc(FS_SIZE);
u32int tempLoc = kmalloc(initrd_end - initrd_location); //random size, make it defined
/*size = the size of the initrd module (address of end - address of start),
* end and start are defined by the bootloader*/
memcpy(tempLoc, location, initrd_end - initrd_location);
// Initialise the main and file header pointers and populate the root directory.
initrd_header = (initrd_header_t *)tempLoc; //first part of location is the number of headers (in struct)
//the location offset with the struct that contains the number of headers
file_headers = (initrd_file_header_t *)(tempLoc + sizeof(initrd_header_t));
// Initialise the root directory.
initrd_root = (fs_node_t*)kmalloc(sizeof(fs_node_t));
strcpy(initrd_root->name, "/");
initrd_root->magic = M_VFS;
initrd_root->mask = initrd_root->uid = initrd_root->gid = initrd_root->inode = initrd_root->length = 0;
initrd_root->flags = FS_DIRECTORY;
initrd_root->read = 0;
initrd_root->write = 0;
initrd_root->readdir = &initrd_readdir;
initrd_root->finddir = &initrd_finddir;
initrd_root->ptr = 0;
initrd_root->impl = 0;
//allocate space for the root nodes, default 32KB size
root_nodes = (fs_node_t*)kmalloc(sizeof(fs_node_t) * (0x8000));
nroot_nodes = initrd_header->nfiles;
// For every file...
u32int i, a, allocSize, nBlocks;
u32int block;
for(i = 0; i < initrd_header->nfiles; i++)
{
// Edit the file's header - currently it holds the file offset
// relative to the start of the ramdisk. We want it relative to the start
// of memory.
file_headers[i].offset += tempLoc;
// Create a new file node.
strcpy(root_nodes[i].name, &file_headers[i].name);
root_nodes[i].magic = M_VFS;
root_nodes[i].mask = 0b110110100; //user rw, group rw, other r
root_nodes[i].uid = root_nodes[i].gid = 0;
root_nodes[i].length = 0;
//~ root_nodes[i].length = file_headers[i].length;
root_nodes[i].inode = i;
root_nodes[i].flags = FS_FILE;
root_nodes[i].read = &initrd_read;
root_nodes[i].write = &initrd_write;
root_nodes[i].readdir = 0;
root_nodes[i].finddir = 0;
root_nodes[i].impl = 0;
//calculates the number of blocks this file has
nBlocks = ((u32int)((file_headers[i].length - 1) / BLOCK_SIZE) + 1);
for(a = 0; a < nBlocks; a++)
{
/* /\* This section copies the file's data into the blocks of the node
* *
* * ((u32int)(root_nodes[i].length / BLOCK_SIZE) + 1) calculates the
* * number of blocks this file will take up at a given length
* * the rootnode[i].length -1 is to offset that the first bit is at position 0*\/
* for(a = 0; a < nBlocks; a++)
* {
* /\*This section allocates memory for any initial sets apart from
* * the direct blocks, as by default, the set pointers in fs_node_t
* * typedef point to nowhere *\/
* //if this file only has a singly set
* if(a >= BLOCKS_DIRECT && a < BLOCKS_DIRECT + BLOCKS_SINGLY)
* {
* //allocate the singly typedef
* if(!root_nodes[i].singly)
* {
* root_nodes[i].singly = (u32int*)kmalloc(BLOCK_SIZE);
*
* //clear the singly block of any junk
* memset(root_nodes[i].singly, 0x0, BLOCK_SIZE);
* }
*
* //if this file has a singly set and a doubly set
* }else if(a >= BLOCKS_DIRECT + BLOCKS_SINGLY &&
* a < BLOCKS_DIRECT + BLOCKS_SINGLY + BLOCKS_DOUBLY)
* {
* //allocate the doubly typedef
* if(!root_nodes[i].doubly)
* {
* root_nodes[i].doubly = (u32int*)kmalloc(BLOCK_SIZE);
*
* //clear the doubly block of any junk
* memset(root_nodes[i].doubly, 0x0, BLOCK_SIZE);
* }
* //the doubly_offset is the offset of the doubly block's node pointing towards the singly block
* u32int doubly_offset;
* doubly_offset = (a - (BLOCKS_DIRECT + BLOCKS_SINGLY)) / BLOCKS_SINGLY;
*
* //allocate the singly typedef
* if(!*(root_nodes[i].doubly + doubly_offset))
* *(root_nodes[i].doubly + doubly_offset) = kmalloc(BLOCK_SIZE);
*
* //if this file has a singly set, a doubly set, and a triply set
* }else if(a >= BLOCKS_DIRECT + BLOCKS_SINGLY + BLOCKS_DOUBLY&&
* a < BLOCKS_DIRECT + BLOCKS_SINGLY + BLOCKS_DOUBLY + BLOCKS_TRIPLY)
* {
*
* //allocate the triply typedef
* if(!root_nodes[i].triply)
* root_nodes[i].triply = (u32int*)kmalloc(BLOCK_SIZE);
*
* //disregard the other blocks
* u32int offset = a - (BLOCKS_DIRECT + BLOCKS_SINGLY + BLOCKS_DOUBLY);
*
* /\*trpily_offset is the offset in the triply block of the node pointing to the doubly block,
* * the doubly_offset is the offset inside the doubly block of the triply block that points to the
* * singly block*\/
*
* u32int triply_offset = (offset) / BLOCKS_DOUBLY;
* u32int doubly_offset = (offset % BLOCKS_DOUBLY) / BLOCKS_DOUBLY;
*
* //allocate the doubly typedef
* if(!*(root_nodes[i].triply + triply_offset))
* *(root_nodes[i].triply + triply_offset) = kmalloc(BLOCK_SIZE);
*
* //allocate the singly typedef
* if(!*((u32int*)*(root_nodes[i].triply + triply_offset) + doubly_offset))
* *((u32int*)*(root_nodes[i].triply + triply_offset) + doubly_offset) = kmalloc(BLOCK_SIZE);
*
* } */
//~ k_printf("a is : %d, size %d\n", a, file_headers[i].length);
//get the size of data to copy
allocSize = blockSizeAtIndex(file_headers[i].length, a, 0);
expand_node(&root_nodes[i], allocSize);
//get the address of the block to write to
block = (u32int)block_of_set(&root_nodes[i], a);
/*The following examples assume that we are in the direct blocks of the node
* the concept is the same for the indirect blocks
*
* (u32int*)block points to the address of the rootnodes[i].blocks[a]
* e.g. &rootnodes[i].blocks[a]
*
* then the *(u32int*)block is the value of that address, i.e. it impersonates
* that it (u32int block) is rootnodes[i].blocks[a], although
* they are found at different memory locations, same concept with hard links */
//allocate space for a block
*(u32int*)block = kmalloc(BLOCK_SIZE);
//copy the data to that block
memcpy(*(u32int*)block, file_headers[i].offset + a * BLOCK_SIZE, allocSize);
}
}
initrd_dev = vfs_createDirectory(initrd_root, "/");
addHardLinkToDir(initrd_dev, initrd_dev, "."); //adds hardlink for root
addHardLinkToDir(initrd_dev, initrd_dev, ".."); //adds hardlink for root
setCurrentDir(initrd_dev);
//create the /dev directory for the virtual files
fs_node_t *dev = vfs_createDirectory(initrd_dev, "dev");
//create and open the stdin, stdout, and stderr files and file descriptors
fs_node_t *stdin = vfs_createFile(dev, "stdin", 1024);
fs_node_t *stdout = vfs_createFile(dev, "stdout", 1024);
fs_node_t *stderr = vfs_createFile(dev, "stderr", 1024);
//create the /etc directory
fs_node_t *etc = vfs_createDirectory(initrd_dev, "etc");
//set the initial file descriptor
initial_fdesc = (file_desc_t*)kmalloc(sizeof(file_desc_t));
//set the mask for "rw", read and write
initial_fdesc->permisions = FDESC_READ | FDESC_WRITE;
initial_fdesc->node = stdin;
initial_fdesc->next = 0;
//open the std files, stdin has alreadt been open when setting the initial file_desc
if(!f_open("stdout", dev, "rw") || !f_open("stderr", dev, "rw"))
{
//some sort of error
kfree((void*)tempLoc);
return 0;
}
//assigns all of the files that were in the file_headers to this dev directory
for(i = 0; i < initrd_header->nfiles; i++)
addFileToDir(initrd_dev, &root_nodes[i]);
kfree((void*)tempLoc);
return initrd_dev;
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct sqlConnection *conn = NULL;
char *command = NULL;
optionInit(&argc, argv, options);
database = optionVal("database", database);
sqlPath = optionVal("sqlPath", sqlPath);
if (argc < 2)
usage();
command = argv[1];
if (argc >= 3)
setCurrentDir(argv[2]);
conn = sqlConnect(database);
if (sameWord(command,"INIT"))
{
if (argc != 2)
usage();
errAbort("INIT is probably too dangerous. DO NOT USE.");
/*
init(conn);
*/
}
else if (sameWord(command,"POP"))
{
if (argc != 2)
usage();
/* populate vgPrb where missing */
populateMissingVgPrb(conn);
}
else if (sameWord(command,"SEQ"))
{
if (argc != 4)
usage();
/* make fake probe sequences */
makeFakeProbeSeq(conn,argv[3]);
}
else if (sameWord(command,"ALI"))
{
if (argc != 4)
usage();
/* blat anything left that is not aligned,
nor even attempted */
doAlignments(conn,argv[3]);
}
else if (sameWord(command,"EXT"))
{
if (argc != 4)
usage();
/* update seq and extfile as necessary */
doSeqAndExtFile(conn,argv[3],"vgProbes");
}
else if (sameWord(command,"PSLMAP"))
{
if (argc != 5)
usage();
/* pslMap anything left that is not aligned,
nor even attempted */
doAlignmentsPslMap(conn,argv[3],argv[4]);
}
else if (sameWord(command,"REMAP"))
{
if (argc != 7)
usage();
/* re-map anything in track specified that is not aligned,
nor even attempted yet, using specified fasta file. */
doAlignmentsReMap(conn,argv[3],argv[4],argv[5],argv[6]);
}
else if (sameWord(command,"SELFMAP"))
{
if (argc != 4)
usage();
/* re-map anything in track specified that is not aligned,
nor even attempted yet, using specified fasta file. */
doAlignmentsSelfMap(conn,argv[3]);
}
else if (sameWord(command,"EXTALL"))
{
if (argc != 4)
usage();
/* update seq and extfile as necessary */
doSeqAndExtFile(conn,argv[3],"vgAllProbes");
}
else
usage();
sqlDisconnect(&conn);
return 0;
}
/**
* Reads the style template info stored in the given (XML) file and creates style templates (OpenGL display lists).
* Existing templates remain where they are but are replaced if a new definition with an existing name is found.
*
* @param filename The name of the file to load.
* @param variables A set of name/value pairs to be replaced in the xml text.
* @return Returns GC_NO_ERROR if everything was ok, otherwise an error code.
*/
TGCError CGenericCanvas::addStylesFromFile(const char* filename, map<wstring, wstring>& variables)
{
TGCError result = GC_NO_ERROR;
xmlNodePtr root, current;
CSVGParser parser;
xmlDocPtr document = NULL;
string currentDir = getCurrentDir();
if (!variables.empty())
{
char *data;
size_t length;
data= preprocessFile(filename, variables, length);
if (data)
{
document = xmlParseMemory(data, (int) length);
free(data);
}
}
else
document = xmlParseFile(utf8ToANSI(filename).c_str());
if (document == NULL)
return GC_XML_PARSE_ERROR;
root = xmlDocGetRootElement(document);
if (root == NULL)
{
xmlFreeDoc(document);
error(this, "XML Error: Template file is empty.");
return GC_XML_EMPTY_DOCUMENT;
}
if (!XML_IS(root, "gc-styles"))
{
xmlFreeDoc(document);
error(this, "XML Error: Template file invalid.");
return GC_XML_INVALID_DOCUMENT;
}
// Switch to the directory of the given file. This is necessary to make relative file names working.
string path = extractFilePath(filename);
setCurrentDir(path);
// Parse description elements.
glMatrixMode(GL_MODELVIEW);
current = root->children;
while (current != NULL)
{
// Be flexible, ignore any unknown layout entries.
if (XML_IS(current, "style-definition"))
{
parser.parseDefinition(current, FModel);
}
else
if (XML_IS(current, "texture"))
{
// Adds a new texture to the texture list.
parseTextureEntry(current, FModel);
checkError();
};
current = current->next;
}
setCurrentDir(currentDir);
xmlFreeDoc(document);
return result;
}
void cdwFakeManifestFromSubmit(char *submitIdString, char *outDir)
/* cdwFakeManifestFromSubmit - Create a fake submission based on a real one that is in the warehouse. */
{
struct sqlConnection *conn = cdwConnect();
char query[512];
sqlSafef(query, sizeof(query), "select * from cdwSubmit where id=%s", submitIdString);
struct cdwSubmit *submit = cdwSubmitLoadByQuery(conn, query);
if (submit == NULL)
errAbort("Can't find submission %s", submitIdString);
uglyf("%d files in query\n", submit->newFiles);
sqlSafef(query, sizeof(query), "select * from cdwFile where submitId=%s", submitIdString);
struct cdwFile *ef, *efList = cdwFileLoadByQuery(conn, query);
FILE *maniF = NULL, *valiF = NULL;
for (ef = efList; ef != NULL; ef = ef->next)
{
struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
if (vf != NULL)
{
/* First time through create out directory and open output files. */
if (maniF == NULL)
{
char *fakeVersion = "##validateManifest version 1.7";
makeDirsOnPath(outDir);
setCurrentDir(outDir);
maniF = mustOpen("manifest.txt", "w");
printSharedHeader(maniF);
fprintf(maniF, "\n");
fprintf(maniF, "%s\n", fakeVersion);
valiF = mustOpen("validated.txt", "w");
printSharedHeader(valiF);
fprintf(valiF, "\tmd5_sum\tsize\tmodified\tvalid_key\n");
fprintf(valiF, "%s\n", fakeVersion);
}
/* Figure out file names */
char cdwPath[PATH_LEN], rootName[FILENAME_LEN], ext[FILEEXT_LEN];
safef(cdwPath, sizeof(cdwPath), "%s%s", cdwRootDir, ef->cdwFileName);
splitPath(ef->cdwFileName, NULL, rootName, ext);
char localPath[PATH_LEN];
safef(localPath, sizeof(localPath), "%s%s", rootName, ext);
/* Create sym-linked file and write to manifest */
symlink(cdwPath, localPath);
fprint2(maniF, valiF, "%s", localPath);
/* Write other columns shared between manifest and validated */
fprint2(maniF, valiF, "\t%s", vf->format);
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->outputType));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->experiment));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->enrichedIn));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->ucscDb));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->replicate));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->part));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->pairedEnd));
fprintf(maniF, "\n");
/* Print out remaining fields in validated.txt */
fprintf(valiF, "\t%s\t%lld\t%lld\n", ef->md5, ef->size, ef->updateTime);
}
}
carefulClose(&maniF);
carefulClose(&valiF);
}
axStatus axFileSystem::setCurrentDirSameAsFile ( const wchar_t* filename ) {
axStringW_<256> str;
axFilePath::dirName( str, filename );
return setCurrentDir( str );
}
