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- /*
- * nvbio
- * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * * Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * * Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * * Neither the name of the NVIDIA CORPORATION nor the
- * names of its contributors may be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
- #include <nvbio-aln-diff/se_analyzer.h>
- #include <nvbio-aln-diff/pe_analyzer.h>
- #include <nvbio-aln-diff/alignment.h>
- #include <nvbio-aln-diff/utils.h>
- #include <nvbio/basic/types.h>
- #include <nvbio/basic/console.h>
- #include <nvbio/basic/html.h>
- #include <nvbio/basic/shared_pointer.h>
- #include <cuda_runtime_api.h>
- #include <vector_types.h>
- #include <vector_functions.h>
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <vector>
- #include <string>
- void crcInit();
- using namespace nvbio;
- using namespace alndiff;
- int main(int argc, char* argv[])
- {
- crcInit();
- int cuda_device = -1;
- int device_count;
- cudaGetDeviceCount(&device_count);
- log_verbose(stderr, " cuda devices : %d\n", device_count);
- const char* report_name = NULL;
- const char* filter_name = NULL;
- uint32 filter_flags = Filter::ALL;
- uint32 filter_stats = Filter::ALL;
- int32 filter_delta = 5;
- bool paired = false;
- bool id_check = true;
- int arg = 1;
- while (arg < argc)
- {
- if (strcmp( argv[arg], "-device" ) == 0)
- {
- cuda_device = atoi(argv[++arg]);
- ++arg;
- }
- else if (strcmp( argv[arg], "-paired" ) == 0)
- {
- paired = true;
- ++arg;
- }
- else if (strcmp( argv[arg], "-report" ) == 0)
- {
- report_name = argv[++arg];
- ++arg;
- }
- else if (strcmp( argv[arg], "-no-ids" ) == 0)
- {
- id_check = false;
- ++arg;
- }
- else if (strcmp( argv[arg], "-filter" ) == 0)
- {
- filter_name = argv[++arg];
- const std::string flags_string( argv[++arg] );
- const std::string stats_string( argv[++arg] );
- filter_delta = atoi(argv[++arg]);
- ++arg;
- char temp[256];
- // parse the filter flags
- const char* begin = flags_string.c_str();
- const char* end = begin;
- filter_flags = 0u;
- while (1)
- {
- while (*end != '|' && *end != '\0')
- {
- temp[end - begin] = *end;
- end++;
- }
- temp[end - begin] = '\0';
- if (strcmp( temp, "distant" ) == 0)
- filter_flags |= Filter::DISTANT;
- else if (strcmp( temp, "discordant" ) == 0)
- filter_flags |= Filter::DISCORDANT;
- else if (strcmp( temp, "diff-ref" ) == 0)
- filter_flags |= Filter::DIFFERENT_REF;
- if (*end == '\0')
- break;
- ++end; begin = end;
- }
- // parse the filter stats
- begin = stats_string.c_str();
- end = begin;
- filter_stats = 0u;
- while (1)
- {
- while (*end != '|' && *end != '\0')
- {
- temp[end - begin] = *end;
- end++;
- }
- temp[end - begin] = '\0';
- if (strcmp( temp, "ed" ) == 0)
- filter_stats |= Filter::ED;
- else if (strcmp( temp, "mapQ" ) == 0)
- filter_stats |= Filter::MAPQ;
- else if (strcmp( temp, "mms" ) == 0)
- filter_stats |= Filter::MMS;
- else if (strcmp( temp, "ins" ) == 0)
- filter_stats |= Filter::INS;
- else if (strcmp( temp, "dels" ) == 0)
- filter_stats |= Filter::DELS;
- if (*end == '\0')
- break;
- ++end; begin = end;
- }
- }
- else
- break;
- }
- // inspect and select cuda devices
- if (device_count)
- {
- if (cuda_device == -1)
- {
- int best_device = 0;
- cudaDeviceProp best_device_prop;
- cudaGetDeviceProperties( &best_device_prop, best_device );
- for (int device = 0; device < device_count; ++device)
- {
- cudaDeviceProp device_prop;
- cudaGetDeviceProperties( &device_prop, device );
- log_verbose(stderr, " device %d has compute capability %d.%d\n", device, device_prop.major, device_prop.minor);
- log_verbose(stderr, " SM count : %u\n", device_prop.multiProcessorCount);
- log_verbose(stderr, " SM clock rate : %u Mhz\n", device_prop.clockRate / 1000);
- log_verbose(stderr, " memory clock rate : %.1f Ghz\n", float(device_prop.memoryClockRate) * 1.0e-6f);
- if (device_prop.major >= best_device_prop.major &&
- device_prop.minor >= best_device_prop.minor)
- {
- best_device_prop = device_prop;
- best_device = device;
- }
- }
- cuda_device = best_device;
- }
- log_verbose(stderr, " chosen device %d\n", cuda_device);
- {
- cudaDeviceProp device_prop;
- cudaGetDeviceProperties( &device_prop, cuda_device );
- log_verbose(stderr, " device name : %s\n", device_prop.name);
- log_verbose(stderr, " compute capability : %d.%d\n", device_prop.major, device_prop.minor);
- }
- cudaSetDevice( cuda_device );
- }
- if (argc < arg + 2)
- {
- log_info(stderr, "nvbio-aln-diff [OPTIONS] <file1> <file2>\n");
- log_info(stderr, "OPTIONS:\n");
- log_info(stderr, " -paired # paired-end input\n" );
- log_info(stderr, " -no-ids # do not perform id checks\n" );
- log_info(stderr, " -report <file-name> # HTML report\n" );
- log_info(stderr, " -filter <file-name>\n" );
- log_info(stderr, " <flags={distant|discordant|diff-ref}>\n" );
- log_info(stderr, " <stats={ed|mapQ|mms|ins|dels}>\n" );
- log_info(stderr, " int:delta\n" );
- return 0;
- }
- if (filter_name)
- {
- std::string filter_flags_string;
- if (filter_flags & Filter::DISTANT)
- filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "distant";
- if (filter_flags & Filter::DISCORDANT)
- filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "discordant";
- if (filter_flags & Filter::DIFFERENT_REF)
- filter_flags_string += std::string(filter_flags_string.length() ? "|" : "") + "diff-ref";
- std::string filter_stats_string;
- if (filter_stats & Filter::ED)
- filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "ed";
- if (filter_stats & Filter::MAPQ)
- filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "mapQ";
- if (filter_stats & Filter::MMS)
- filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "mms";
- if (filter_stats & Filter::INS)
- filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "ins";
- if (filter_stats & Filter::DELS)
- filter_stats_string += std::string(filter_stats_string.length() ? "|" : "") + "dels";
- log_info(stderr, "filter file : %s\n", filter_name);
- log_info(stderr, " flags : %s\n", filter_flags_string.c_str());
- log_info(stderr, " stats : %s\n", filter_stats_string.c_str());
- log_info(stderr, " delta : %d\n", filter_delta);
- }
- if (argc == arg + 2)
- {
- const char *aln_file_nameL = argv[arg];
- const char *aln_file_nameR = argv[arg+1];
- if (paired)
- {
- const char *aln_file_nameL = argv[arg];
- const char *aln_file_nameR = argv[arg+1];
- SharedPointer<AlignmentStream> aln_streamL = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameL ) );
- SharedPointer<AlignmentStream> aln_streamR = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameR ) );
- if (aln_streamL == NULL || aln_streamL->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL); exit(1); }
- if (aln_streamR == NULL || aln_streamR->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR); exit(1); }
- const uint32 BATCH_SIZE = 500000;
- std::vector<Alignment> batchL( BATCH_SIZE );
- std::vector<Alignment> batchR( BATCH_SIZE );
- Filter filter( filter_name, filter_flags, filter_stats, filter_delta );
- SharedPointer<PEAnalyzer> analyzer = SharedPointer<PEAnalyzer>( new PEAnalyzer( filter, id_check ) );
- uint32 n_batch = 0;
- while (1)
- {
- const uint32 batch_sizeL = aln_streamL->next_batch( BATCH_SIZE, &batchL[0] );
- const uint32 batch_sizeR = aln_streamR->next_batch( BATCH_SIZE, &batchR[0] );
- const uint32 min_batch_size = nvbio::min( batch_sizeL, batch_sizeR );
- const uint32 max_batch_size = nvbio::max( batch_sizeL, batch_sizeR );
- if (min_batch_size != max_batch_size)
- log_warning(stderr, "alignment files have different size\n");
- log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f);
- for (uint32 i = 0; i < min_batch_size; i += 2)
- {
- const Alignment* alnL1 = &batchL[i];
- const Alignment* alnL2 = &batchL[i+1];
- const Alignment* alnR1 = &batchR[i];
- const Alignment* alnR2 = &batchR[i+1];
- if (alnL1->is_mapped() && alnL1->mate == alnL2->mate)
- {
- log_error(stderr, "alignments %u and %u in \"%s\" refer to the same mate, must come from different reads\n", i, i+1, aln_file_nameL);
- return 1;
- }
- if (alnR1->is_mapped() && alnR1->mate == alnR2->mate)
- {
- log_error(stderr, "alignments %u and %u in \"%s\" refer to the same mate, must come from different reads\n", i, i+1, aln_file_nameR);
- return 1;
- }
- if (alnL1->mate) std::swap( alnL1, alnL2 );
- if (alnR1->mate) std::swap( alnR1, alnR2 );
- analyzer->push(
- AlignmentPair( *alnL1, *alnL2 ),
- AlignmentPair( *alnR1, *alnR2 ));
- }
- if (report_name)
- analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name );
- analyzer->flush();
- log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched());
- log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L());
- log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R());
- log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R());
- log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R());
- log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L());
- log_verbose(stderr, " paired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L());
- log_verbose(stderr, " paired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R());
- log_verbose(stderr, " paired [L&R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_and_R());
- log_verbose(stderr, " paired/unpaired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_not_R());
- log_verbose(stderr, " paired/unpaired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R_not_L());
- log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref());
- log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant());
- log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant());
- log_verbose(stderr, " filtered : %u\n", analyzer->filtered());
- if (min_batch_size < BATCH_SIZE)
- break;
- ++n_batch;
- }
- }
- else
- {
- SharedPointer<AlignmentStream> aln_streamL = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameL ) );
- SharedPointer<AlignmentStream> aln_streamR = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameR ) );
- if (aln_streamL == NULL || aln_streamL->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL); exit(1); }
- if (aln_streamR == NULL || aln_streamR->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR); exit(1); }
- const uint32 BATCH_SIZE = 500000;
- std::vector<Alignment> batchL( BATCH_SIZE );
- std::vector<Alignment> batchR( BATCH_SIZE );
- Filter filter( filter_name, filter_flags, filter_stats, filter_delta );
- SharedPointer<SEAnalyzer> analyzer = SharedPointer<SEAnalyzer>( new SEAnalyzer( filter ) );
- uint32 n_batch = 0;
- while (1)
- {
- const uint32 batch_sizeL = aln_streamL->next_batch( BATCH_SIZE, &batchL[0] );
- const uint32 batch_sizeR = aln_streamR->next_batch( BATCH_SIZE, &batchR[0] );
- if (batch_sizeL != batch_sizeR)
- log_warning(stderr, "alignment files have different size\n");
- const uint32 min_batch_size = nvbio::min( batch_sizeL, batch_sizeR );
- log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f);
- for (uint32 i = 0; i < min_batch_size; ++i)
- analyzer->push( batchL[i], batchR[i] );
- if (report_name)
- analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name );
- analyzer->flush();
- log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched());
- log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L());
- log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R());
- log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R());
- log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R());
- log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L());
- log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref());
- log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant());
- log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant());
- log_verbose(stderr, " filtered : %u\n", analyzer->filtered());
- if (min_batch_size < BATCH_SIZE)
- break;
- ++n_batch;
- }
- }
- }
- else if (argc == arg + 4)
- {
- const char *aln_file_nameL1 = argv[arg];
- const char *aln_file_nameL2 = argv[arg+1];
- const char *aln_file_nameR1 = argv[arg+2];
- const char *aln_file_nameR2 = argv[arg+3];
- const char* aln_file_nameL = aln_file_nameL1;
- const char* aln_file_nameR = aln_file_nameR1;
- SharedPointer<AlignmentStream> aln_streamL1 = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameL1 ) );
- SharedPointer<AlignmentStream> aln_streamL2 = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameL2 ) );
- SharedPointer<AlignmentStream> aln_streamR1 = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameR1 ) );
- SharedPointer<AlignmentStream> aln_streamR2 = SharedPointer<AlignmentStream>( open_alignment_file( aln_file_nameR2 ) );
- if (aln_streamL1 == NULL || aln_streamL1->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL1); exit(1); }
- if (aln_streamL2 == NULL || aln_streamL2->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameL2); exit(1); }
- if (aln_streamR2 == NULL || aln_streamR1->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR1); exit(1); }
- if (aln_streamR2 == NULL || aln_streamR2->is_ok() == false) { log_error(stderr, "failed opening \"%s\"\n", aln_file_nameR2); exit(1); }
- const uint32 BATCH_SIZE = 500000;
- std::vector<Alignment> batchL1( BATCH_SIZE );
- std::vector<Alignment> batchL2( BATCH_SIZE );
- std::vector<Alignment> batchR1( BATCH_SIZE );
- std::vector<Alignment> batchR2( BATCH_SIZE );
- Filter filter( filter_name, filter_flags, filter_stats, filter_delta );
- SharedPointer<PEAnalyzer> analyzer = SharedPointer<PEAnalyzer>( new PEAnalyzer( filter, id_check ) );
- uint32 n_batch = 0;
- while (1)
- {
- const uint32 batch_sizeL1 = aln_streamL1->next_batch( BATCH_SIZE, &batchL1[0] );
- const uint32 batch_sizeL2 = aln_streamL2->next_batch( BATCH_SIZE, &batchL2[0] );
- const uint32 batch_sizeR1 = aln_streamR1->next_batch( BATCH_SIZE, &batchR1[0] );
- const uint32 batch_sizeR2 = aln_streamR2->next_batch( BATCH_SIZE, &batchR2[0] );
- const uint32 min_batch_size = nvbio::min(
- nvbio::min( batch_sizeL1, batch_sizeL2 ),
- nvbio::min( batch_sizeR1, batch_sizeR2 ) );
- const uint32 max_batch_size = nvbio::min(
- nvbio::max( batch_sizeL1, batch_sizeL2 ),
- nvbio::max( batch_sizeR1, batch_sizeR2 ) );
- if (min_batch_size != max_batch_size)
- log_warning(stderr, "alignment files have different size\n");
- log_info(stderr, "analizing batch[%u]: %u alignments (%.1f M)\n", n_batch, min_batch_size, float(n_batch * BATCH_SIZE + min_batch_size)*1.0e-6f);
- for (uint32 i = 0; i < min_batch_size; ++i)
- analyzer->push(
- AlignmentPair( batchL1[i], batchL2[i] ),
- AlignmentPair( batchR1[i], batchR2[i] ));
- if (report_name)
- analyzer->generate_report( aln_file_nameL, aln_file_nameR, report_name );
- analyzer->flush();
- log_verbose(stderr, " mismatched : %5.2f%%\n", 100.0f * analyzer->mismatched());
- log_verbose(stderr, " mapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L());
- log_verbose(stderr, " mapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R());
- log_verbose(stderr, " mapped [L&R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_and_R());
- log_verbose(stderr, " mapped/unmapped [L] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_L_not_R());
- log_verbose(stderr, " mapped/unmapped [R] : %5.2f%%\n", 100.0f * analyzer->mapped.avg_R_not_L());
- log_verbose(stderr, " paired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L());
- log_verbose(stderr, " paired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R());
- log_verbose(stderr, " paired [L&R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_and_R());
- log_verbose(stderr, " paired/unpaired [L] : %5.2f%%\n", 100.0f * analyzer->paired.avg_L_not_R());
- log_verbose(stderr, " paired/unpaired [R] : %5.2f%%\n", 100.0f * analyzer->paired.avg_R_not_L());
- log_verbose(stderr, " different ref : %5.2f%%\n", 100.0f * analyzer->different_ref());
- log_verbose(stderr, " distant : %5.2f%%\n", 100.0f * analyzer->distant());
- log_verbose(stderr, " discordant : %5.2f%%\n", 100.0f * analyzer->discordant());
- log_verbose(stderr, " filtered : %u\n", analyzer->filtered());
- if (min_batch_size < BATCH_SIZE)
- break;
- ++n_batch;
- }
- }
- cudaDeviceReset();
- return 0;
- }
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