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Accelerate preprocess #71

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Accelerate preprocess #71

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b110e94
small fix
Mar 13, 2021
e5c9701
accelarate preprocess
Apr 3, 2021
0c5a352
add more options to scan_alignments
Apr 13, 2021
9b41956
small fix
Apr 17, 2021
4a99dc4
small fix
Jun 30, 2021
239c99c
fix for is_none
Jul 14, 2021
344a0e5
fix for missed ensemble positions
Jul 20, 2021
625469f
small fix
Jul 20, 2021
7071d4e
small fix
Jul 22, 2021
c0af977
small fix
Aug 11, 2021
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557 changes: 464 additions & 93 deletions neusomatic/cpp/scan_alignments.cpp
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80 changes: 74 additions & 6 deletions neusomatic/include/Options.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,20 +16,26 @@ namespace neusomatic {
{"ref", required_argument, 0, 'r'},
{"calculate_qual_stat", no_argument, 0, 'c'},
{"min_mapq", required_argument, 0, 'q'},
{"min_af", required_argument, 0, 'a'},
{"snp_min_bq", required_argument, 0, 'n'},
{"snp_min_af", required_argument, 0, 'a'},
{"ins_min_af", required_argument, 0, 'i'},
{"del_min_af", required_argument, 0, 'l'},
{"snp_min_ao", required_argument, 0, 'M'},
{"out_vcf_file", required_argument, 0, 'f'},
{"out_count_file", required_argument, 0, 'o'},
{"fully_contained", no_argument, 0, 'y'},
{"window_size", required_argument, 0, 'w'},
{"num_threads", required_argument, 0, 't'},
{"max_depth", required_argument, 0, 'd'},
{"min_depth", required_argument, 0, 'h'},
{"include_secondary", no_argument, 0, 's'},
{"filter_duplicate", no_argument, 0, 'D'},
{"filter_QCfailed", no_argument, 0, 'Q'},
{"filter_improper_pair", no_argument, 0, 'E'},
{"filter_mate_unmapped", no_argument, 0, 'F'},
{"filter_improper_orientation", no_argument, 0, 'G'},
{"report_all_alleles", no_argument, 0, 'A'},
{"report_count_for_all_positions", no_argument, 0, 'C'},
{0, 0, 0, 0} // terminator
};

Expand All @@ -46,20 +52,26 @@ namespace neusomatic {
std::cerr<< "-r/--ref, reference file path, required.\n";
std::cerr<< "-c/--calculate_qual_stat, calculating base quality and other stats, default False.\n";
std::cerr<< "-q/--min_mapq, minimum mapping quality, default 0.\n";
std::cerr<< "-a/--min_af, minimum allele freq, default 0.1.\n";
std::cerr<< "-n/--snp_min_bq, SNP minimum base quality, default 10.\n";
std::cerr<< "-a/--snp_min_af, SNP minimum allele freq, default 0.01.\n";
std::cerr<< "-i/--ins_min_af, INS minimum allele freq, default 0.01.\n";
std::cerr<< "-l/--del_min_af, DEL minimum allele freq, default 0.01.\n";
std::cerr<< "-M/--snp_min_ao, SNP minimum alternate count for low AF candidates, default 3.\n";
std::cerr<< "-f/--out_vcf_file, output vcf file path, required.\n";
std::cerr<< "-o/--out_count_file, output count file path, required.\n";
std::cerr<< "-w/--window_size, window size to scan the variants, default is 15.\n";
std::cerr<< "-y/--fully_contained, if this option is on. A read has to be fully contained in the region, default is False.\n";
// std::cerr<< "-t/--num_threads, number or thread used for building the count matrix, default is 4.\n";
std::cerr<< "-d/--max_depth, maximum depth for building the count matrix, default is 40,000.\n";
std::cerr<< "-h/--min_depth, minimum depth for building the count matrix, default is 0.\n";
std::cerr<< "-s/--include_secondary, consider secondary alignments, default is False.\n";
std::cerr<< "-D/--filter_duplicate, filter duplicate reads if the flag is set, default is False.\n";
std::cerr<< "-Q/--filter_QCfailed, filter QC failed reads if the flag is set, default is False.\n";
std::cerr<< "-E/--filter_improper_pair, filter improper pairs if the flag is set, default is False.\n";
std::cerr<< "-F/--filter_mate_unmapped, filter reads with unmapeed mates if the flag is set, default is False.\n";
std::cerr<< "-G/--filter_improper_orientation, filter reads with improper orientation (not FR) or different chrom, default is False.\n";
std::cerr<< "-A/--report_all_alleles, report all alleles per column, default is False.\n";
std::cerr<< "-C/--report_count_for_all_positions, report counts for all positions, default is False.\n";
}

int parseInt(const char* optarg, int lower, const char *errmsg, void (*print_help)()) {
Expand Down Expand Up @@ -132,12 +144,18 @@ namespace neusomatic {
case 'q':
opt.min_mapq() = parseInt(optarg, 0, "-q/--min_mapq must be at least 0", print_help);
break;
case 'n':
opt.snp_min_bq() = parseInt(optarg, 0, "-n/--snp_min_bq must be at least 0", print_help);
break;
case 'f':
opt.vcf_out() = optarg;
break;
case 'd':
opt.max_depth() = parseInt(optarg, 1, "-d/--max_depth must be at least 1", print_help);
break;
case 'h':
opt.min_depth() = parseInt(optarg, 1, "-h/--min_depth must be at least 1", print_help);
break;
case 'o':
opt.count_out() = optarg;
break;
Expand Down Expand Up @@ -168,8 +186,20 @@ namespace neusomatic {
case 'A':
opt.report_all_alleles() = true;
break;
case 'C':
opt.report_count_for_all_positions() = true;
break;
case 'a':
opt.min_allele_freq() = parseFloat(optarg, 0.0, 1.0, "-a/--min_af must be between 0 and 1", print_help);
opt.snp_min_allele_freq() = parseFloat(optarg, 0.0, 1.0, "-a/--snp_min_af must be between 0 and 1", print_help);
break;
case 'i':
opt.ins_min_allele_freq() = parseFloat(optarg, 0.0, 1.0, "-i/--ins_min_af must be between 0 and 1", print_help);
break;
case 'l':
opt.del_min_allele_freq() = parseFloat(optarg, 0.0, 1.0, "-l/--del_min_af must be between 0 and 1", print_help);
break;
case 'M':
opt.snp_min_ao() = parseInt(optarg, 1, "-M/--snp_min_ao must be at least 1", print_help);
break;
case 't':
//opt.num_threads() = parseInt(optarg, 1, "-t/--num_threads must be at least 1", print_help);
Expand Down Expand Up @@ -262,10 +292,18 @@ struct Options {
return (min_mapq_);
}

decltype(auto) snp_min_bq() const {
return (snp_min_bq_);
}

decltype(auto) min_mapq() {
return (min_mapq_);
}

decltype(auto) snp_min_bq() {
return (snp_min_bq_);
}

decltype(auto) calculate_qual_stat() {
return (calculate_qual_stat_);
}
Expand All @@ -274,8 +312,20 @@ struct Options {
return (window_size_);
}

decltype(auto) min_allele_freq() {
return (min_allele_freq_);
decltype(auto) snp_min_allele_freq() {
return (snp_min_allele_freq_);
}

decltype(auto) ins_min_allele_freq() {
return (ins_min_allele_freq_);
}

decltype(auto) del_min_allele_freq() {
return (del_min_allele_freq_);
}

decltype(auto) snp_min_ao() {
return (snp_min_ao_);
}

decltype(auto) fully_contained() {
Expand All @@ -286,6 +336,10 @@ struct Options {
return (max_depth_);
}

decltype(auto) min_depth() {
return (min_depth_);
}

decltype(auto) include_secondary() {
return (include_secondary_);
}
Expand Down Expand Up @@ -342,6 +396,14 @@ struct Options {
return (report_all_alleles_);
}

decltype(auto) report_count_for_all_positions() const {
return (report_count_for_all_positions_);
}

decltype(auto) report_count_for_all_positions() {
return (report_count_for_all_positions_);
}

private:
unsigned verbosity_ = 0;
std::string bam_in_;
Expand All @@ -352,18 +414,24 @@ struct Options {
std::string ref_;
bool calculate_qual_stat_ = false;
bool fully_contained_ = false;
float min_allele_freq_ = 0.01;
float snp_min_allele_freq_ = 0.01;
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Such constants should be declared somewhere else. Things like these would be good candidates for refactoring the code.

float ins_min_allele_freq_ = 0.01;
float del_min_allele_freq_ = 0.01;
int snp_min_ao_ = 3;
int min_mapq_ = 0;
int snp_min_bq_ = 0;
int window_size_ = 500;
int num_threads_ = 1;
int max_depth_ = 5000000;
int min_depth_ = 0;
bool include_secondary_ = false;
bool filter_duplicate_ = false;
bool filter_QCfailed_ = false;
bool filter_improper_pair_ = false;
bool filter_mate_unmapped_ = false;
bool filter_improper_orientation_ = false;
bool report_all_alleles_ = false;
bool report_count_for_all_positions_ = false;
};
}//namespace neusomatic

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