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cuffnorm.cpp
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cuffnorm.cpp
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/*
* cuffdiff.cpp
* cufflinks
*
* Created by Cole Trapnell on 10/21/09.
* Copyright 2009 Cole Trapnell. All rights reserved.
*
*/
#include <stdlib.h>
#include <getopt.h>
#include <string>
#include <numeric>
#include <cfloat>
#include <iostream>
#include "common.h"
#include "hits.h"
#include "bundles.h"
#include "abundances.h"
#include "tokenize.h"
#include "biascorrection.h"
#include "update_check.h"
#include <boost/thread.hpp>
#include <boost/version.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/graph/graph_traits.hpp>
#include <boost/numeric/ublas/matrix.hpp>
#include <boost/numeric/ublas/matrix_proxy.hpp>
#include <boost/numeric/ublas/vector.hpp>
#include <boost/numeric/ublas/vector_proxy.hpp>
#include <boost/numeric/ublas/io.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/random/mersenne_twister.hpp>
#include "differential.h"
extern "C" {
#include "locfit/local.h"
}
// Need at least this many reads in a locus to do any testing on it
vector<string> sample_labels;
double FDR = 0.05;
bool samples_are_time_series = false;
using namespace std;
using namespace boost;
// We leave out the short codes for options that don't take an argument
#if ENABLE_THREADS
const char *short_options = "m:p:s:c:I:j:L:M:o:b:TNqvuF:C:";
#else
const char *short_options = "m:s:c:I:j:L:M:o:b:TNqvuF:C:";
#endif
static struct option long_options[] = {
{"labels", required_argument, 0, 'L'},
{"seed", required_argument, 0, OPT_RANDOM_SEED},
{"norm-standards-file", required_argument, 0, OPT_NORM_STANDARDS_FILE},
{"use-sample-sheet", no_argument, 0, OPT_USE_SAMPLE_SHEET},
{"output-dir", required_argument, 0, 'o'},
{"verbose", no_argument, 0, 'v'},
{"quiet", no_argument, 0, 'q'},
#if ENABLE_THREADS
{"num-threads", required_argument, 0, 'p'},
#endif
{"library-type", required_argument, 0, OPT_LIBRARY_TYPE},
{"no-update-check", no_argument, 0, OPT_NO_UPDATE_CHECK},
{"compatible-hits-norm", no_argument, 0, OPT_USE_COMPAT_MASS},
{"total-hits-norm", no_argument, 0, OPT_USE_TOTAL_MASS},
// Some options for testing different stats policies
{"max-bundle-frags", required_argument, 0, OPT_MAX_FRAGS_PER_BUNDLE},
{"library-norm-method", required_argument, 0, OPT_LIB_NORM_METHOD},
{"output-format", required_argument, 0, OPT_OUTPUT_FORMAT},
{0, 0, 0, 0} // terminator
};
void print_usage()
{
fprintf(stderr, "cuffnorm v%s (%s)\n", PACKAGE_VERSION, SVN_REVISION);
fprintf(stderr, "-----------------------------\n");
//NOTE: SPACES ONLY, bozo
fprintf(stderr, "Usage: cuffnorm [options] <transcripts.gtf> <sample1_expr.cxb> <sample2_expr.cxb> [... sampleN_expr.cxb]\n");
fprintf(stderr, " Supply replicate CXB files as comma separated lists for each condition: sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb\n");
fprintf(stderr, "General Options:\n");
fprintf(stderr, " -o/--output-dir write all output files to this directory [ default: ./ ]\n");
fprintf(stderr, " -L/--labels comma-separated list of condition labels\n");
fprintf(stderr, " --norm-standards-file Housekeeping/spike genes to normalize libraries [ default: NULL ]\n"); // NOT YET DOCUMENTED, keep secret for now
#if ENABLE_THREADS
fprintf(stderr, " -p/--num-threads number of threads used during quantification [ default: 1 ]\n");
#endif
fprintf(stderr, " --library-type Library prep used for input reads [ default: below ]\n");
fprintf(stderr, " --library-norm-method Method used to normalize library sizes [ default: below ]\n");
fprintf(stderr, " --output-format Format for output tables [ default: below ]\n");
fprintf(stderr, "\nAdvanced Options:\n");
fprintf(stderr, " --compatible-hits-norm count hits compatible with reference RNAs only [ default: TRUE ]\n");
fprintf(stderr, " --total-hits-norm count all hits for normalization [ default: FALSE ]\n");
fprintf(stderr, " -v/--verbose log-friendly verbose processing (no progress bar) [ default: FALSE ]\n");
fprintf(stderr, " -q/--quiet log-friendly quiet processing (no progress bar) [ default: FALSE ]\n");
fprintf(stderr, " --seed value of random number generator seed [ default: 0 ]\n");
fprintf(stderr, " --no-update-check do not contact server to check for update availability[ default: FALSE ]\n");
print_library_table();
print_lib_norm_method_table();
print_output_format_table();
}
int parse_options(int argc, char** argv)
{
int option_index = 0;
int next_option;
string sample_label_list;
string dispersion_method_str;
string lib_norm_method_str;
string output_format_str;
do {
next_option = getopt_long_only(argc, argv, short_options, long_options, &option_index);
if (next_option == -1) /* Done with options. */
break;
switch (next_option) {
case 0:
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
break;
case 'p':
num_threads = (uint32_t)parseInt(1, "-p/--num-threads arg must be at least 1", print_usage);
break;
case 'F':
min_isoform_fraction = parseFloat(0, 1.0, "-F/--min-isoform-fraction must be between 0 and 1.0", print_usage);
break;
case 'L':
sample_label_list = optarg;
break;
case OPT_NORM_STANDARDS_FILE:
{
norm_standards_filename = optarg;
break;
}
case OPT_USE_SAMPLE_SHEET:
{
use_sample_sheet = true;
break;
}
case 'v':
{
if (cuff_quiet)
{
fprintf(stderr, "Warning: Can't be both verbose and quiet! Setting verbose only.\n");
}
cuff_quiet = false;
cuff_verbose = true;
break;
}
case 'q':
{
if (cuff_verbose)
{
fprintf(stderr, "Warning: Can't be both verbose and quiet! Setting quiet only.\n");
}
cuff_verbose = false;
cuff_quiet = true;
break;
}
case 'o':
{
output_dir = optarg;
break;
}
case OPT_LIBRARY_TYPE:
{
library_type = optarg;
break;
}
case OPT_NO_UPDATE_CHECK:
{
no_update_check = true;
break;
}
case OPT_RANDOM_SEED:
{
random_seed = parseInt(0, "--seed must be at least 0", print_usage);
break;
}
case OPT_USE_COMPAT_MASS:
{
use_compat_mass = true;
break;
}
case OPT_USE_TOTAL_MASS:
{
use_total_mass = true;
break;
}
case OPT_LIB_NORM_METHOD:
{
lib_norm_method_str = optarg;
break;
}
case OPT_OUTPUT_FORMAT:
{
output_format_str = optarg;
break;
}
default:
print_usage();
return 1;
}
} while(next_option != -1);
if (library_type != "")
{
map<string, ReadGroupProperties>::iterator lib_itr =
library_type_table.find(library_type);
if (lib_itr == library_type_table.end())
{
fprintf(stderr, "Error: Library type %s not supported\n", library_type.c_str());
exit(1);
}
else
{
if (library_type == "transfrags")
{
allow_junk_filtering = false;
}
global_read_properties = &lib_itr->second;
}
}
else
{
}
// Set the count dispersion method to use
if (dispersion_method_str == "")
{
dispersion_method_str = default_dispersion_method;
}
map<string, DispersionMethod>::iterator disp_itr =
dispersion_method_table.find(dispersion_method_str);
if (disp_itr == dispersion_method_table.end())
{
fprintf(stderr, "Error: Dispersion method %s not supported\n", dispersion_method_str.c_str());
exit(1);
}
else
{
dispersion_method = disp_itr->second;
}
// Set the library size normalization method to use
if (lib_norm_method_str == "")
{
lib_norm_method_str = default_lib_norm_method;
}
map<string, LibNormalizationMethod>::iterator lib_norm_itr =
lib_norm_method_table.find(lib_norm_method_str);
if (lib_norm_itr == lib_norm_method_table.end())
{
fprintf(stderr, "Error: Normalization method %s not supported\n", lib_norm_method_str.c_str());
exit(1);
}
else
{
lib_norm_method = lib_norm_itr->second;
}
// Set the count dispersion method to use
if (output_format_str == "")
{
output_format_str = default_output_format;
}
map<string, OutputFormat>::iterator output_itr =
output_format_table.find(output_format_str);
if (output_itr == output_format_table.end())
{
fprintf(stderr, "Error: Output format %s not supported\n", output_format_str.c_str());
exit(1);
}
else
{
output_format = output_itr->second;
}
if (use_total_mass && use_compat_mass)
{
fprintf (stderr, "Error: please supply only one of --compatibile-hits-norm and --total-hits-norm\n");
exit(1);
}
tokenize(sample_label_list, ",", sample_labels);
allow_junk_filtering = false;
return 0;
}
#if ENABLE_THREADS
boost::mutex inspect_lock;
#endif
void inspect_map_worker(ReplicatedBundleFactory& fac,
int& tmp_min_frag_len,
int& tmp_max_frag_len,
IdToLocusMap& id_to_locus_map)
{
#if ENABLE_THREADS
boost::this_thread::at_thread_exit(decr_pool_count);
#endif
int min_f = std::numeric_limits<int>::max();
int max_f = 0;
fac.inspect_replicate_maps(min_f, max_f, id_to_locus_map);
#if ENABLE_THREADS
inspect_lock.lock();
#endif
tmp_min_frag_len = min(min_f, tmp_min_frag_len);
tmp_max_frag_len = max(max_f, tmp_max_frag_len);
#if ENABLE_THREADS
inspect_lock.unlock();
#endif
}
boost::shared_ptr<TrackingDataWriter> tracking_data_writer;
bool quantitate_next_locus(const RefSequenceTable& rt,
vector<boost::shared_ptr<ReplicatedBundleFactory> >& bundle_factories,
boost::shared_ptr<TestLauncher> launcher)
{
for (size_t i = 0; i < bundle_factories.size(); ++i)
{
boost::shared_ptr<SampleAbundances> s_ab = boost::shared_ptr<SampleAbundances>(new SampleAbundances);
#if ENABLE_THREADS
while(1)
{
locus_thread_pool_lock.lock();
if (locus_curr_threads < locus_num_threads)
{
break;
}
locus_thread_pool_lock.unlock();
boost::this_thread::sleep(boost::posix_time::milliseconds(5));
}
locus_curr_threads++;
locus_thread_pool_lock.unlock();
boost::shared_ptr<HitBundle> pBundle = boost::shared_ptr<HitBundle>(new HitBundle());
bool non_empty = bundle_factories[i]->next_bundle(*pBundle, true);
if (pBundle->compatible_mass() > 0)
{
thread quantitate(sample_worker,
non_empty,
pBundle,
boost::ref(rt),
boost::ref(*(bundle_factories[i])),
s_ab,
i,
launcher,
false);
}
else
{
sample_worker(non_empty,
pBundle,
boost::ref(rt),
boost::ref(*(bundle_factories[i])),
s_ab,
i,
launcher,
false);
locus_thread_pool_lock.lock();
locus_curr_threads--;
locus_thread_pool_lock.unlock();
}
#else
HitBundle bundle;
bool non_empty = sample_factory.next_bundle(bundle);
sample_worker(non_emtpy,
pBundle,
boost::ref(rt),
boost::ref(*(bundle_factories[i])),
s_ab,
i,
launcher,
false);
#endif
}
return true;
}
void parse_sample_sheet_file(FILE* sample_sheet_file,
vector<string>& sample_labels,
vector<string>& sam_hit_filename_lists)
{
char pBuf[10 * 1024];
size_t non_blank_lines_read = 0;
sample_labels.clear();
map<string, vector<string> > sample_groups;
while (fgets(pBuf, 10*1024, sample_sheet_file))
{
if (strlen(pBuf) > 0)
{
char* nl = strchr(pBuf, '\n');
if (nl)
*nl = 0;
string pBufstr = pBuf;
string trimmed = boost::trim_copy(pBufstr);
if (trimmed.length() > 0 && trimmed[0] != '#')
{
non_blank_lines_read++;
vector<string> columns;
tokenize(trimmed, "\t", columns);
if (non_blank_lines_read == 1)
continue;
if (columns.size() < 2)
{
if (columns.size() > 0)
fprintf(stderr, "Malformed record in sample sheet: \n > %s\n", pBuf);
else
continue;
}
string sam_file = columns[0];
string sample_group = columns[1];
pair<map<string, vector<string> >::iterator, bool> inserted = sample_groups.insert(make_pair(sample_group, vector<string>()));
inserted.first->second.push_back(sam_file);
}
}
}
for (map<string, vector<string> >::iterator itr = sample_groups.begin();
itr != sample_groups.end(); ++itr)
{
sample_labels.push_back(itr->first);
string sam_list = boost::join(itr->second, ",");
sam_hit_filename_lists.push_back(sam_list);
}
}
void parse_norm_standards_file(FILE* norm_standards_file)
{
char pBuf[10 * 1024];
size_t non_blank_lines_read = 0;
boost::shared_ptr<map<string, LibNormStandards> > norm_standards(new map<string, LibNormStandards>);
while (fgets(pBuf, 10*1024, norm_standards_file))
{
if (strlen(pBuf) > 0)
{
char* nl = strchr(pBuf, '\n');
if (nl)
*nl = 0;
string pBufstr = pBuf;
string trimmed = boost::trim_copy(pBufstr);
if (trimmed.length() > 0 && trimmed[0] != '#')
{
non_blank_lines_read++;
vector<string> columns;
tokenize(trimmed, "\t", columns);
if (non_blank_lines_read == 1)
continue;
if (columns.size() < 1) //
{
continue;
}
string gene_id = columns[0];
LibNormStandards L;
norm_standards->insert(make_pair(gene_id, L));
}
}
}
lib_norm_standards = norm_standards;
}
void print_variability_models(FILE* var_model_out, const vector<boost::shared_ptr<ReplicatedBundleFactory> >& factories)
{
fprintf(var_model_out, "condition\tlocus\tcompatible_count_mean\tcompatible_count_var\ttotal_count_mean\ttotal_count_var\tfitted_var\n");
for (size_t i = 0; i < factories.size(); ++i)
{
string factor_name = factories[i]->condition_name();
boost::shared_ptr<ReadGroupProperties> rg = factories[i]->factories()[0]->read_group_properties();
boost::shared_ptr<MassDispersionModel const> model = rg->mass_dispersion_model();
// const vector<double>& means = model->scaled_compatible_mass_means();
// const vector<double>& raw_vars = model->scaled_compatible_variances();
const vector<LocusCount>& common_scale_compatible_counts = rg->common_scale_compatible_counts();
for (size_t j = 0; j < common_scale_compatible_counts.size(); ++j)
{
string locus_desc = common_scale_compatible_counts[j].locus_desc;
pair<double, double> compat_mean_and_var = model->get_compatible_mean_and_var(locus_desc);
pair<double, double> total_mean_and_var = model->get_total_mean_and_var(locus_desc);
// double total_compat_count = 0;
// if (itr != locus_to_total_count_table.end())
// total_compat_count = itr->second.count;
fprintf(var_model_out, "%s\t%s\t%lg\t%lg\t%lg\t%lg\t%lg\n",
factor_name.c_str(),
locus_desc.c_str(),
compat_mean_and_var.first,
compat_mean_and_var.second,
total_mean_and_var.first,
total_mean_and_var.second,
model->scale_mass_variance(compat_mean_and_var.first));
}
}
fclose(var_model_out);
}
void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_standards_file, vector<string>& sam_hit_filename_lists, Outfiles& outfiles)
{
ReadTable it;
RefSequenceTable rt(true, false);
vector<boost::shared_ptr<Scaffold> > ref_mRNAs;
vector<boost::shared_ptr<ReplicatedBundleFactory> > bundle_factories;
vector<boost::shared_ptr<ReadGroupProperties> > all_read_groups;
set<boost::shared_ptr<ReadGroupProperties> > serialized_read_groups;
for (size_t i = 0; i < sam_hit_filename_lists.size(); ++i)
{
vector<string> sam_hit_filenames;
tokenize(sam_hit_filename_lists[i], ",", sam_hit_filenames);
vector<boost::shared_ptr<BundleFactory> > replicate_factories;
string condition_name = sample_labels[i];
for (size_t j = 0; j < sam_hit_filenames.size(); ++j)
{
boost::shared_ptr<HitFactory> hs;
boost::shared_ptr<BundleFactory> hf;
try
{
hs = boost::shared_ptr<HitFactory>(new PrecomputedExpressionHitFactory(sam_hit_filenames[j], it, rt));
hf = boost::shared_ptr<BundleFactory>(new PrecomputedExpressionBundleFactory(static_pointer_cast<PrecomputedExpressionHitFactory>(hs)));
}
catch(boost::archive::archive_exception & e)
{
hs = boost::shared_ptr<HitFactory>(createSamHitFactory(sam_hit_filenames[j], it, rt));
hf = boost::shared_ptr<BundleFactory>(new BundleFactory(hs, REF_DRIVEN));
}
boost::shared_ptr<ReadGroupProperties> rg_props(new ReadGroupProperties);
if (global_read_properties)
{
*rg_props = *global_read_properties;
}
else
{
*rg_props = hs->read_group_properties();
}
rg_props->checked_parameters(hs->read_group_properties().checked_parameters());
rg_props->condition_name(condition_name);
rg_props->replicate_num(j);
rg_props->file_path(sam_hit_filenames[j]);
all_read_groups.push_back(rg_props);
hf->read_group_properties(rg_props);
replicate_factories.push_back(hf);
//replicate_factories.back()->set_ref_rnas(ref_mRNAs);
}
bundle_factories.push_back(boost::shared_ptr<ReplicatedBundleFactory>(new ReplicatedBundleFactory(replicate_factories, condition_name)));
}
boost::crc_32_type ref_gtf_crc_result;
::load_ref_rnas(ref_gtf, rt, ref_mRNAs, ref_gtf_crc_result, corr_bias, false);
if (ref_mRNAs.empty())
return;
vector<boost::shared_ptr<Scaffold> > mask_rnas;
if (mask_gtf)
{
boost::crc_32_type mask_gtf_crc_result;
::load_ref_rnas(mask_gtf, rt, mask_rnas, mask_gtf_crc_result, false, false);
}
BOOST_FOREACH (boost::shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
{
// NOTE: we aren't deep copying here to save memory. We can pull this off
// because unless bias correction or multiread correction is enabled,
// we don't need to write into Scaffold objects.
fac->set_ref_rnas(ref_mRNAs, false);
if (mask_gtf)
fac->set_mask_rnas(mask_rnas);
}
if (norm_standards_file != NULL)
{
parse_norm_standards_file(norm_standards_file);
}
validate_cross_sample_parameters(all_read_groups);
vector<pair<size_t, size_t > > contrasts;
#if ENABLE_THREADS
locus_num_threads = num_threads;
#endif
int tmp_min_frag_len = numeric_limits<int>::max();
int tmp_max_frag_len = 0;
boost::shared_ptr<IdToLocusMap> id_to_locus_map(new IdToLocusMap(boost::shared_ptr<map<string, set<string> > >(new map<string, set<string> >())));
ProgressBar p_bar("Inspecting maps and determining fragment length distributions.",0);
BOOST_FOREACH (boost::shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
{
#if ENABLE_THREADS
while(1)
{
locus_thread_pool_lock.lock();
if (locus_curr_threads < locus_num_threads)
{
break;
}
locus_thread_pool_lock.unlock();
boost::this_thread::sleep(boost::posix_time::milliseconds(5));
}
locus_curr_threads++;
locus_thread_pool_lock.unlock();
thread inspect(inspect_map_worker,
boost::ref(*fac),
boost::ref(tmp_min_frag_len),
boost::ref(tmp_max_frag_len),
boost::ref(*id_to_locus_map));
#else
inspect_map_worker(boost::ref(*fac),
boost::ref(tmp_min_frag_len),
boost::ref(tmp_max_frag_len),
boost::ref(*id_to_locus_map));
#endif
}
// wait for the workers to finish up before reporting everthing.
#if ENABLE_THREADS
while(1)
{
locus_thread_pool_lock.lock();
if (locus_curr_threads == 0)
{
locus_thread_pool_lock.unlock();
break;
}
locus_thread_pool_lock.unlock();
boost::this_thread::sleep(boost::posix_time::milliseconds(5));
}
#endif
normalize_counts(all_read_groups);
long double total_norm_mass = 0.0;
long double total_mass = 0.0;
BOOST_FOREACH (boost::shared_ptr<ReadGroupProperties> rg_props, all_read_groups)
{
total_norm_mass += rg_props->normalized_map_mass();
total_mass += rg_props->total_map_mass();
rg_props->clear_count_tables();
}
min_frag_len = tmp_min_frag_len;
max_frag_len = tmp_max_frag_len;
final_est_run = false;
double num_bundles = (double)bundle_factories[0]->num_bundles();
p_bar = ProgressBar("Calculating preliminary abundance estimates", num_bundles);
Tracking tracking;
final_est_run = true;
p_bar = ProgressBar("Normalizing expression levels for locus", num_bundles);
tracking_data_writer = boost::shared_ptr<TrackingDataWriter>(new TrackingDataWriter(bundle_factories.size(), &outfiles, &tracking, all_read_groups, sample_labels, &p_bar, id_to_locus_map));
while (true)
{
//boost::shared_ptr<vector<boost::shared_ptr<SampleAbundances> > > abundances(new vector<boost::shared_ptr<SampleAbundances> >());
quantitate_next_locus(rt, bundle_factories, tracking_data_writer);
bool more_loci_remain = false;
BOOST_FOREACH (boost::shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories)
{
if (rep_fac->bundles_remain())
{
more_loci_remain = true;
break;
}
}
if (!more_loci_remain)
{
// wait for the workers to finish up before doing the cross-sample testing.
#if ENABLE_THREADS
while(1)
{
locus_thread_pool_lock.lock();
if (locus_curr_threads == 0)
{
locus_thread_pool_lock.unlock();
break;
}
locus_thread_pool_lock.unlock();
boost::this_thread::sleep(boost::posix_time::milliseconds(5));
}
#endif
break;
}
}
p_bar.complete();
}
void open_outfiles_for_writing_cuffdiff_format(Outfiles& outfiles)
{
static const int filename_buf_size = 2048;
char isoform_fpkm_tracking_name[filename_buf_size];
sprintf(isoform_fpkm_tracking_name, "%s/isoforms.fpkm_tracking", output_dir.c_str());
FILE* isoform_fpkm_out = fopen(isoform_fpkm_tracking_name, "w");
if (!isoform_fpkm_out)
{
fprintf(stderr, "Error: cannot open isoform-level FPKM tracking file %s for writing\n",
isoform_fpkm_tracking_name);
exit(1);
}
outfiles.isoform_fpkm_tracking_out = isoform_fpkm_out;
char tss_group_fpkm_tracking_name[filename_buf_size];
sprintf(tss_group_fpkm_tracking_name, "%s/tss_groups.fpkm_tracking", output_dir.c_str());
FILE* tss_group_fpkm_out = fopen(tss_group_fpkm_tracking_name, "w");
if (!tss_group_fpkm_out)
{
fprintf(stderr, "Error: cannot open TSS group-level FPKM tracking file %s for writing\n",
tss_group_fpkm_tracking_name);
exit(1);
}
outfiles.tss_group_fpkm_tracking_out = tss_group_fpkm_out;
char cds_fpkm_tracking_name[filename_buf_size];
sprintf(cds_fpkm_tracking_name, "%s/cds.fpkm_tracking", output_dir.c_str());
FILE* cds_fpkm_out = fopen(cds_fpkm_tracking_name, "w");
if (!cds_fpkm_out)
{
fprintf(stderr, "Error: cannot open CDS level FPKM tracking file %s for writing\n",
cds_fpkm_tracking_name);
exit(1);
}
outfiles.cds_fpkm_tracking_out = cds_fpkm_out;
char gene_fpkm_tracking_name[filename_buf_size];
sprintf(gene_fpkm_tracking_name, "%s/genes.fpkm_tracking", output_dir.c_str());
FILE* gene_fpkm_out = fopen(gene_fpkm_tracking_name, "w");
if (!gene_fpkm_out)
{
fprintf(stderr, "Error: cannot open gene-level FPKM tracking file %s for writing\n",
gene_fpkm_tracking_name);
exit(1);
}
outfiles.gene_fpkm_tracking_out = gene_fpkm_out;
char isoform_count_tracking_name[filename_buf_size];
sprintf(isoform_count_tracking_name, "%s/isoforms.count_tracking", output_dir.c_str());
FILE* isoform_count_out = fopen(isoform_count_tracking_name, "w");
if (!isoform_count_out)
{
fprintf(stderr, "Error: cannot open isoform-level count tracking file %s for writing\n",
isoform_count_tracking_name);
exit(1);
}
outfiles.isoform_count_tracking_out = isoform_count_out;
char tss_group_count_tracking_name[filename_buf_size];
sprintf(tss_group_count_tracking_name, "%s/tss_groups.count_tracking", output_dir.c_str());
FILE* tss_group_count_out = fopen(tss_group_count_tracking_name, "w");
if (!tss_group_count_out)
{
fprintf(stderr, "Error: cannot open TSS group-level count tracking file %s for writing\n",
tss_group_count_tracking_name);
exit(1);
}
outfiles.tss_group_count_tracking_out = tss_group_count_out;
char cds_count_tracking_name[filename_buf_size];
sprintf(cds_count_tracking_name, "%s/cds.count_tracking", output_dir.c_str());
FILE* cds_count_out = fopen(cds_count_tracking_name, "w");
if (!cds_count_out)
{
fprintf(stderr, "Error: cannot open CDS level count tracking file %s for writing\n",
cds_count_tracking_name);
exit(1);
}
outfiles.cds_count_tracking_out = cds_count_out;
char gene_count_tracking_name[filename_buf_size];
sprintf(gene_count_tracking_name, "%s/genes.count_tracking", output_dir.c_str());
FILE* gene_count_out = fopen(gene_count_tracking_name, "w");
if (!gene_count_out)
{
fprintf(stderr, "Error: cannot open gene-level count tracking file %s for writing\n",
gene_count_tracking_name);
exit(1);
}
outfiles.gene_count_tracking_out = gene_count_out;
char isoform_rep_tracking_name[filename_buf_size];
sprintf(isoform_rep_tracking_name, "%s/isoforms.read_group_tracking", output_dir.c_str());
FILE* isoform_rep_out = fopen(isoform_rep_tracking_name, "w");
if (!isoform_rep_out)
{
fprintf(stderr, "Error: cannot open isoform-level read group tracking file %s for writing\n",
isoform_rep_tracking_name);
exit(1);
}
outfiles.isoform_rep_tracking_out = isoform_rep_out;
char tss_group_rep_tracking_name[filename_buf_size];
sprintf(tss_group_rep_tracking_name, "%s/tss_groups.read_group_tracking", output_dir.c_str());
FILE* tss_group_rep_out = fopen(tss_group_rep_tracking_name, "w");
if (!tss_group_rep_out)
{
fprintf(stderr, "Error: cannot open TSS group-level read group tracking file %s for writing\n",
tss_group_rep_tracking_name);
exit(1);
}
outfiles.tss_group_rep_tracking_out = tss_group_rep_out;
char cds_rep_tracking_name[filename_buf_size];
sprintf(cds_rep_tracking_name, "%s/cds.read_group_tracking", output_dir.c_str());
FILE* cds_rep_out = fopen(cds_rep_tracking_name, "w");
if (!cds_rep_out)
{
fprintf(stderr, "Error: cannot open CDS level read group tracking file %s for writing\n",
cds_rep_tracking_name);
exit(1);
}
outfiles.cds_rep_tracking_out = cds_rep_out;
char gene_rep_tracking_name[filename_buf_size];
sprintf(gene_rep_tracking_name, "%s/genes.read_group_tracking", output_dir.c_str());
FILE* gene_rep_out = fopen(gene_rep_tracking_name, "w");
if (!gene_rep_out)
{
fprintf(stderr, "Error: cannot open gene-level read group tracking file %s for writing\n",
gene_rep_tracking_name);
exit(1);
}
outfiles.gene_rep_tracking_out = gene_rep_out;
char read_group_info_name[filename_buf_size];
sprintf(read_group_info_name, "%s/read_groups.info", output_dir.c_str());
FILE* read_group_out = fopen(read_group_info_name, "w");
if (!read_group_out)
{
fprintf(stderr, "Error: cannot open read group info file %s for writing\n",
read_group_info_name);
exit(1);
}
outfiles.read_group_info_out = read_group_out;
char run_info_name[filename_buf_size];
sprintf(run_info_name, "%s/run.info", output_dir.c_str());
FILE* run_info_out = fopen(run_info_name, "w");
if (!run_info_out)
{
fprintf(stderr, "Error: cannot open run info file %s for writing\n",
run_info_name);
exit(1);
}
outfiles.run_info_out = run_info_out;
}
void open_outfiles_for_writing_simple_table_format(Outfiles& outfiles)
{
static const int filename_buf_size = 2048;
char isoform_fpkm_tracking_name[filename_buf_size];
sprintf(isoform_fpkm_tracking_name, "%s/isoforms.fpkm_table", output_dir.c_str());
FILE* isoform_fpkm_out = fopen(isoform_fpkm_tracking_name, "w");
if (!isoform_fpkm_out)
{
fprintf(stderr, "Error: cannot open isoform-level FPKM table %s for writing\n",
isoform_fpkm_tracking_name);
exit(1);
}
outfiles.isoform_fpkm_tracking_out = isoform_fpkm_out;
char tss_group_fpkm_tracking_name[filename_buf_size];
sprintf(tss_group_fpkm_tracking_name, "%s/tss_groups.fpkm_table", output_dir.c_str());
FILE* tss_group_fpkm_out = fopen(tss_group_fpkm_tracking_name, "w");
if (!tss_group_fpkm_out)
{
fprintf(stderr, "Error: cannot open TSS group-level FPKM table %s for writing\n",
tss_group_fpkm_tracking_name);
exit(1);
}
outfiles.tss_group_fpkm_tracking_out = tss_group_fpkm_out;
char cds_fpkm_tracking_name[filename_buf_size];
sprintf(cds_fpkm_tracking_name, "%s/cds.fpkm_table", output_dir.c_str());
FILE* cds_fpkm_out = fopen(cds_fpkm_tracking_name, "w");
if (!cds_fpkm_out)
{
fprintf(stderr, "Error: cannot open CDS level FPKM table %s for writing\n",
cds_fpkm_tracking_name);
exit(1);
}
outfiles.cds_fpkm_tracking_out = cds_fpkm_out;
char gene_fpkm_tracking_name[filename_buf_size];
sprintf(gene_fpkm_tracking_name, "%s/genes.fpkm_table", output_dir.c_str());
FILE* gene_fpkm_out = fopen(gene_fpkm_tracking_name, "w");
if (!gene_fpkm_out)
{
fprintf(stderr, "Error: cannot open gene-level FPKM table %s for writing\n",
gene_fpkm_tracking_name);
exit(1);
}
outfiles.gene_fpkm_tracking_out = gene_fpkm_out;
char isoform_count_tracking_name[filename_buf_size];
sprintf(isoform_count_tracking_name, "%s/isoforms.count_table", output_dir.c_str());
FILE* isoform_count_out = fopen(isoform_count_tracking_name, "w");
if (!isoform_count_out)
{
fprintf(stderr, "Error: cannot open isoform-level count table %s for writing\n",
isoform_count_tracking_name);
exit(1);
}
outfiles.isoform_count_tracking_out = isoform_count_out;
char tss_group_count_tracking_name[filename_buf_size];
sprintf(tss_group_count_tracking_name, "%s/tss_groups.count_table", output_dir.c_str());
FILE* tss_group_count_out = fopen(tss_group_count_tracking_name, "w");
if (!tss_group_count_out)
{
fprintf(stderr, "Error: cannot open TSS group-level count table %s for writing\n",