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[WIP] Enable automatic detecting and loading all filter/sketch types #1717

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[WIP] Enable automatic detecting and loading all filter/sketch types #1717

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4f5e3f4
Replace ad hoc defines with an enumerated type
standage Jun 1, 2017
eb95593
Merge branch 'master' into fix/sketchload
standage Jun 2, 2017
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13 changes: 10 additions & 3 deletions include/oxli/oxli.hh
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Original file line number Diff line number Diff line change
Expand Up @@ -87,13 +87,20 @@ private:\

# define SAVED_SIGNATURE "OXLI"
# define SAVED_FORMAT_VERSION 4
# define SAVED_COUNTING_HT 1
# define SAVED_HASHBITS 2
# define SAVED_TAGS 3
# define SAVED_STOPTAGS 4
# define SAVED_SUBSET 5
# define SAVED_LABELSET 6
# define SAVED_SMALLCOUNT 7

typedef enum saved_sketch_type {
SAVED_NODETABLE,
SAVED_COUNTTABLE,
SAVED_SMALLCOUNTTABLE,
// The following are set explicitly for backwards compatibility
SAVED_NODEGRAPH = 2,
SAVED_COUNTGRAPH = 1,
SAVED_SMALLCOUNTGRAPH = 7
} saved_sketch_type;

# define TRAVERSAL_LEFT 0
# define TRAVERSAL_RIGHT 1
Expand Down
6 changes: 3 additions & 3 deletions src/khmer/_cpy_khmer.cc
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Expand Up @@ -350,13 +350,13 @@ MOD_INIT(_khmer)
}

PyObject * filetype_dict = Py_BuildValue("{s,i,s,i,s,i,s,i,s,i,s,i,s,i}",
"COUNTING_HT", SAVED_COUNTING_HT,
"HASHBITS", SAVED_HASHBITS,
"COUNTING_HT", SAVED_COUNTGRAPH,
"HASHBITS", SAVED_NODEGRAPH,
"TAGS", SAVED_TAGS,
"STOPTAGS", SAVED_STOPTAGS,
"SUBSET", SAVED_SUBSET,
"LABELSET", SAVED_LABELSET,
"SMALLCOUNT", SAVED_SMALLCOUNT);
"SMALLCOUNT", SAVED_SMALLCOUNTGRAPH);
if (PyModule_AddObject( m, "FILETYPES", filetype_dict ) < 0) {
return MOD_ERROR_VAL;
}
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18 changes: 9 additions & 9 deletions src/oxli/storage.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ void BitStorage::save(std::string outfilename, WordLength ksize)
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);

unsigned char ht_type = SAVED_HASHBITS;
unsigned char ht_type = SAVED_NODEGRAPH;
outfile.write((const char *) &ht_type, 1);

outfile.write((const char *) &save_ksize, sizeof(save_ksize));
Expand Down Expand Up @@ -200,7 +200,7 @@ void BitStorage::load(std::string infilename, WordLength &ksize)
<< " while reading k-mer graph from " << infilename
<< "; should be " << (int) SAVED_FORMAT_VERSION;
throw oxli_file_exception(err.str());
} else if (!(ht_type == SAVED_HASHBITS)) {
} else if (!(ht_type == SAVED_NODEGRAPH)) {
std::ostringstream err;
err << "Incorrect file format type " << (int) ht_type
<< " while reading k-mer graph from " << infilename;
Expand Down Expand Up @@ -330,7 +330,7 @@ ByteStorageFileReader::ByteStorageFileReader(
<< " while reading k-mer count file from " << infilename
<< "; should be " << (int) SAVED_FORMAT_VERSION;
throw oxli_file_exception(err.str());
} else if (!(ht_type == SAVED_COUNTING_HT)) {
} else if (!(ht_type == SAVED_COUNTGRAPH)) {
std::ostringstream err;
err << "Incorrect file format type " << (int) ht_type
<< " while reading k-mer count file from " << infilename;
Expand Down Expand Up @@ -446,15 +446,15 @@ ByteStorageGzFileReader::ByteStorageGzFileReader(
SAVED_SIGNATURE;
throw oxli_file_exception(err.str());
} else if (!(version == SAVED_FORMAT_VERSION)
|| !(ht_type == SAVED_COUNTING_HT)) {
|| !(ht_type == SAVED_COUNTGRAPH)) {
if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading k-mer count file from " << infilename
<< "; should be " << (int) SAVED_FORMAT_VERSION;
gzclose(infile);
throw oxli_file_exception(err.str());
} else if (!(ht_type == SAVED_COUNTING_HT)) {
} else if (!(ht_type == SAVED_COUNTGRAPH)) {
std::ostringstream err;
err << "Incorrect file format type " << (int) ht_type
<< " while reading k-mer count file from " << infilename;
Expand Down Expand Up @@ -599,7 +599,7 @@ ByteStorageFileWriter::ByteStorageFileWriter(
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);

unsigned char ht_type = SAVED_COUNTING_HT;
unsigned char ht_type = SAVED_COUNTGRAPH;
outfile.write((const char *) &ht_type, 1);

unsigned char use_bigcount = 0;
Expand Down Expand Up @@ -666,7 +666,7 @@ ByteStorageGzFileWriter::ByteStorageGzFileWriter(
unsigned char version = SAVED_FORMAT_VERSION;
gzwrite(outfile, (const char *) &version, 1);

unsigned char ht_type = SAVED_COUNTING_HT;
unsigned char ht_type = SAVED_COUNTGRAPH;
gzwrite(outfile, (const char *) &ht_type, 1);

unsigned char use_bigcount = 0;
Expand Down Expand Up @@ -786,7 +786,7 @@ void NibbleStorage::save(std::string outfilename, WordLength ksize)
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);

unsigned char ht_type = SAVED_SMALLCOUNT;
unsigned char ht_type = SAVED_SMALLCOUNTGRAPH;
outfile.write((const char *) &ht_type, 1);

outfile.write((const char *) &save_ksize, sizeof(save_ksize));
Expand Down Expand Up @@ -860,7 +860,7 @@ void NibbleStorage::load(std::string infilename, WordLength& ksize)
<< " while reading k-mer count file from " << infilename
<< "; should be " << (int) SAVED_FORMAT_VERSION;
throw oxli_file_exception(err.str());
} else if (!(ht_type == SAVED_SMALLCOUNT)) {
} else if (!(ht_type == SAVED_SMALLCOUNTGRAPH)) {
std::ostringstream err;
err << "Incorrect file format type " << (int) ht_type
<< " while reading k-mer count file from " << infilename;
Expand Down