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Fix/change output filename format, add options for maps.
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@brianwalenz
brianwalenz committed Dec 1, 2021
1 parent 1c4691d commit efb74aa
Showing 1 changed file with 100 additions and 27 deletions.
127 changes: 100 additions & 27 deletions src/utgcns/layoutToPackage.C
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ void
loadVerkkoLayouts(sqCache *reads,
std::vector<tgTig *> &tigs,
compressedFileReader *layoutFile,
const char *outputPrefix) {
const char *mapPrefix) {

uint32 err = 0;
splitToWords W;
Expand All @@ -48,10 +48,23 @@ loadVerkkoLayouts(sqCache *reads,
uint32 nReads = 0;
char fname[FILENAME_MAX+1];

snprintf(fname, FILENAME_MAX, "%s.tig_names.txt", outputPrefix);
std::ofstream tigNames(fname, std::ofstream::out);
snprintf(fname, FILENAME_MAX, "%s.readNames.txt", outputPrefix);
std::ofstream readNames(fname, std::ofstream::out);
FILE *readMap = AS_UTL_openOutputFile(mapPrefix, '.', "readName_to_ID.map");
FILE *tigMap = AS_UTL_openOutputFile(mapPrefix, '.', "tigName_to_ID.map");

if (readMap) {
fprintf(readMap, " readID tigID read name\n");
fprintf(readMap, "---------- ---------- --------------------\n");
}

if (tigMap) {
fprintf(tigMap, " tigID tig name\n");
fprintf(tigMap, "---------- --------------------\n");
}

//snprintf(fname, FILENAME_MAX, "%s.tig_names.txt", outputPrefix);
//std::ofstream tigNames(fname, std::ofstream::out);
//snprintf(fname, FILENAME_MAX, "%s.readNames.txt", outputPrefix);
//std::ofstream readNames(fname, std::ofstream::out);

// A real tigStore doesn't have a zeroth tig, and we maintain that here by
// adding a nullptr to our list.
Expand All @@ -69,7 +82,9 @@ loadVerkkoLayouts(sqCache *reads,
}
else {
tig->addChild()->set(id, 0, 0, 0, strtouint32(W[1]), strtouint32(W[2]));
readNames << W[0] << "\t" << id << "\t" << tig->tigID() << std::endl;

if (readMap)
fprintf(readMap, "%10u %10u %s\n", id, tig->tigID(), W[0]);
}

nReads--;
Expand All @@ -78,7 +93,10 @@ loadVerkkoLayouts(sqCache *reads,
else if (strcmp(W[0], "tig") == 0) {
#warning still need to save tigName somewhere
tig->_tigID = tigs.size();
tigNames << tig->tigID() << "\t" << W[1] << std::endl;

if (tigMap)
fprintf(tigMap, "%10u %s\n", tig->tigID(), W[1]);

//tig->_tigName = duplicateString(W[1]);
}

Expand Down Expand Up @@ -108,8 +126,9 @@ loadVerkkoLayouts(sqCache *reads,

delete [] line;
delete tig;
tigNames.close();
readNames.close();

AS_UTL_closeFile(tigMap);
AS_UTL_closeFile(readMap);

if (err > 0) {
fprintf(stderr, "ERROR: loading layouts failed, check your input sequences and layout file!");
Expand All @@ -123,7 +142,8 @@ loadVerkkoLayouts(sqCache *reads,
int
main(int argc, char **argv) {
char const *layoutFilename = nullptr;
char const *outputPrefix = nullptr;
char const *outputPattern = nullptr;
char const *mapPrefix = nullptr;

std::vector<char const *> readFilenames;

Expand All @@ -146,7 +166,11 @@ main(int argc, char **argv) {
}

else if (strcmp(argv[arg], "-output") == 0) { // Output package filename
outputPrefix = argv[++arg]; // prefix; prefix.####.package
outputPattern = argv[++arg]; // pattern.
}

else if (strcmp(argv[arg], "-idmap") == 0) { // Output read/tig id map
mapPrefix = argv[++arg]; // filename prefix.
}

else if (strcmp(argv[arg], "-partition") == 0) {
Expand Down Expand Up @@ -181,20 +205,32 @@ main(int argc, char **argv) {
err.push_back(es);
}

if (outputPrefix == nullptr)
err.push_back("ERROR: No output prefix (-output) supplied!\n");
if (outputPattern == nullptr)
err.push_back("ERROR: No output pattern (-output) supplied!\n");

if (err.size() > 0) {
fprintf(stderr, "usage: %s [opts]\n", argv[0]);
fprintf(stderr, "\n");
fprintf(stderr, " INPUT\n");
fprintf(stderr, " -layout l Input layouts.\n");
fprintf(stderr, " -reads a [b ...] Input reads, fasta/fasta, uncompressed/gz/bz2/xz.\n");
fprintf(stderr, " -output p Output prefix.\n");
fprintf(stderr, " -partition s x n Partitioning parameters.\n");
fprintf(stderr, " s - max size of each partition\n");
fprintf(stderr, " x - scaling\n");
fprintf(stderr, " n - max number of reads per partition\n");
fprintf(stderr, " -layout l Input layouts.\n");
fprintf(stderr, " -reads a [b ...] Input reads, fasta/fasta, uncompressed/gz/bz2/xz.\n");
fprintf(stderr, "\n");
fprintf(stderr, " -output name####.cnspack Output file pattern. Must include one or more consecutive '#'\n");
fprintf(stderr, " symbols. These will be replaced with the zero-leading number of\n");
fprintf(stderr, " the package, expanded to fit the number of packages if needed.\n");
fprintf(stderr, " Examples: (assume 173 total packages)\n");
fprintf(stderr, " 'name.cnspack' -> 'name.cnspack001' through 'name.cnspack173'\n");
fprintf(stderr, " 'name#.cnspack' -> 'name001.cnspack' through 'name173.cnspack'\n");
fprintf(stderr, " 'name####.cnspack' -> 'name0001.cnspack' through 'name0173.cnspack'\n");
fprintf(stderr, "\n");
fprintf(stderr, " -idmap prefix Write a mapping of read/tig name <-> read/tig ID to files\n");
fprintf(stderr, " prefix.readName_to_ID.map\n");
fprintf(stderr, " prefix.tigName_to_ID.map\n");
fprintf(stderr, "\n");
fprintf(stderr, " -partition s x n Partitioning parameters.\n");
fprintf(stderr, " s - max size of each partition\n");
fprintf(stderr, " x - scaling\n");
fprintf(stderr, " n - max number of reads per partition\n");
fprintf(stderr, "\n");

for (uint32 ii=0; ii<err.size(); ii++)
Expand Down Expand Up @@ -222,7 +258,7 @@ main(int argc, char **argv) {
std::vector<tgTig *> tigs;
compressedFileReader *layoutFile = new compressedFileReader(layoutFilename);

loadVerkkoLayouts(reads, tigs, layoutFile, outputPrefix);
loadVerkkoLayouts(reads, tigs, layoutFile, mapPrefix);

delete layoutFile;

Expand All @@ -242,18 +278,55 @@ main(int argc, char **argv) {
true);

//
// Output packages for each partition.
// Open packages for each partition.
//

writeBuffer **package = new writeBuffer * [tp._nPartitions];

fprintf(stderr, "-- Opening %u output packages.\n", tp._nPartitions);
{
char packageFormat[FILENAME_MAX+1];
char packageName[FILENAME_MAX+1];
char nDig = '0';
char nSym = '0';

if (tp._nPartitions < 10) nDig = '1'; // Count the number of
else if (tp._nPartitions < 100) nDig = '2'; // digits needed. Simple,
else if (tp._nPartitions < 1000) nDig = '3'; // but ugly.
else if (tp._nPartitions < 10000) nDig = '4';
else nDig = '5';

char const *pp = outputPattern;
uint32 pi = 0;

while ((*pp != 0) && (*pp != '#')) // Copy the output format up
packageFormat[pi++] = *pp++; // to the first '#' symbol.

while ((*pp != 0) && (*pp == '#')) // Count and skip '#' symbols.
nSym++, pp++;

if (nDig < nSym) // If user requested more, use
nDig = nSym; // their value.

for (uint32 pi=0; pi<tp._nPartitions; pi++) {
char packageName[FILENAME_MAX+1];
snprintf(packageName, FILENAME_MAX, "%s.%04u.cnspack", outputPrefix, pi);
if (nDig > '9') // But never more than 9.
nDig = '9';

package[pi] = new writeBuffer(packageName, "w");
packageFormat[pi++] = '%'; // Insert the proper format string.
packageFormat[pi++] = '0';
packageFormat[pi++] = nDig;
packageFormat[pi++] = 'u';

while (*pp != 0) // Copy the rest of the string.
packageFormat[pi++] = *pp++;


fprintf(stderr, "-- Opening %u output packages.\n", tp._nPartitions);

for (uint32 pi=0; pi<tp._nPartitions; pi++) {
snprintf(packageName, FILENAME_MAX, packageFormat, pi);

fprintf(stderr, "-- '%s'\n", packageName);
package[pi] = new writeBuffer(packageName, "w");
}
}

//
Expand Down

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