| 1 |
/* |
| 2 |
* common.cpp |
| 3 |
* TopHat |
| 4 |
* |
| 5 |
* Created by Cole Trapnell on 11/26/08. |
| 6 |
* Copyright 2008 Cole Trapnell. All rights reserved. |
| 7 |
* |
| 8 |
*/ |
| 9 |
|
| 10 |
#ifdef HAVE_CONFIG_H |
| 11 |
#include <config.h> |
| 12 |
#endif |
| 13 |
|
| 14 |
#include <iostream> |
| 15 |
#include <sstream> |
| 16 |
#include <cstdarg> |
| 17 |
#include <limits> |
| 18 |
#include <getopt.h> |
| 19 |
|
| 20 |
#include "common.h" |
| 21 |
|
| 22 |
using namespace std; |
| 23 |
|
| 24 |
#ifdef MEM_DEBUG |
| 25 |
//function for debugging memory usage of current program in Linux |
| 26 |
|
| 27 |
#include <unistd.h> |
| 28 |
#include <ios> |
| 29 |
#include <fstream> |
| 30 |
|
| 31 |
////////////////////////////////////////////////////////////////////////////// |
| 32 |
// process_mem_usage(double &, double &) - takes two doubles by reference, |
| 33 |
// attempts to read the system-dependent data for a process' virtual memory |
| 34 |
// size and resident set size, and return the results in KB. |
| 35 |
// |
| 36 |
// On failure, returns 0.0, 0.0 |
| 37 |
|
| 38 |
void process_mem_usage(double& vm_usage, double& resident_set) { |
| 39 |
using std::ios_base; |
| 40 |
using std::ifstream; |
| 41 |
using std::string; |
| 42 |
vm_usage = 0.0; |
| 43 |
resident_set = 0.0; |
| 44 |
// 'file' stat seems to give the most reliable results |
| 45 |
ifstream stat_stream("/proc/self/stat",ios_base::in); |
| 46 |
// dummy vars for leading entries in stat that we don't care about |
| 47 |
string pid, comm, state, ppid, pgrp, session, tty_nr; |
| 48 |
string tpgid, flags, minflt, cminflt, majflt, cmajflt; |
| 49 |
string utime, stime, cutime, cstime, priority, nice; |
| 50 |
string O, itrealvalue, starttime; |
| 51 |
|
| 52 |
// the two fields we want |
| 53 |
// |
| 54 |
unsigned long vsize; |
| 55 |
long rss; |
| 56 |
|
| 57 |
stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr |
| 58 |
>> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt |
| 59 |
>> utime >> stime >> cutime >> cstime >> priority >> nice |
| 60 |
>> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest |
| 61 |
|
| 62 |
stat_stream.close(); |
| 63 |
|
| 64 |
long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages |
| 65 |
vm_usage = vsize / 1024.0; |
| 66 |
resident_set = rss * page_size_kb; |
| 67 |
} |
| 68 |
|
| 69 |
void print_mem_usage() { |
| 70 |
double vs, rs; |
| 71 |
process_mem_usage(vs,rs); |
| 72 |
vs/=1024; |
| 73 |
rs/=1024; |
| 74 |
fprintf(stderr, "VMSize: %6.1fMB\tRSize: %6.1fMB\n", vs, rs); |
| 75 |
} |
| 76 |
#endif |
| 77 |
|
| 78 |
bool bowtie2 = true; |
| 79 |
int bowtie2_min_score = -10; |
| 80 |
int bowtie2_max_penalty = 6; |
| 81 |
int bowtie2_min_penalty = 2; |
| 82 |
int bowtie2_penalty_for_N = 1; |
| 83 |
int bowtie2_read_gap_open = 5; |
| 84 |
int bowtie2_read_gap_cont = 3; |
| 85 |
int bowtie2_ref_gap_open = 5; |
| 86 |
int bowtie2_ref_gap_cont = 3; |
| 87 |
|
| 88 |
// daehwan - temporary |
| 89 |
bool parallel = true; |
| 90 |
|
| 91 |
unsigned int max_insertion_length = 3; |
| 92 |
unsigned int max_deletion_length = 3; |
| 93 |
|
| 94 |
|
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int inner_dist_mean = 200; |
| 96 |
int inner_dist_std_dev = 20; |
| 97 |
int max_mate_inner_dist = -1; |
| 98 |
|
| 99 |
int min_anchor_len = 8; |
| 100 |
int min_report_intron_length = 50; |
| 101 |
int max_report_intron_length = 500000; |
| 102 |
|
| 103 |
int min_closure_intron_length = 50; |
| 104 |
int max_closure_intron_length = 5000; |
| 105 |
|
| 106 |
int min_coverage_intron_length = 50; |
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int max_coverage_intron_length = 20000; |
| 108 |
|
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int min_segment_intron_length = 50; |
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int max_segment_intron_length = 500000; |
| 111 |
|
| 112 |
uint32_t min_closure_exon_length = 100; |
| 113 |
|
| 114 |
int island_extension = 25; |
| 115 |
int segment_length = 25; |
| 116 |
int segment_mismatches = 2; |
| 117 |
int max_read_mismatches = 2; |
| 118 |
int max_splice_mismatches = 1; |
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|
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ReadFormat reads_format = FASTQ; |
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|
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bool verbose = false; |
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|
| 124 |
unsigned int max_multihits = 20; |
| 125 |
unsigned int max_seg_multihits = 40; |
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bool no_closure_search = false; |
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bool no_coverage_search = false; |
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bool no_microexon_search = false; |
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bool butterfly_search = false; |
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int num_threads = 1; |
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|
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float min_isoform_fraction = 0.15f; |
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|
| 134 |
string output_dir = "tophat_out"; |
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string aux_outfile = ""; //auxiliary output file name (e.g. prep_reads read stats) |
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string index_outfile = ""; |
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string gene_filter = ""; |
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string gff_file = ""; |
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string ium_reads = ""; |
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string sam_header = ""; |
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string sam_readgroup_id = ""; |
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string zpacker = ""; |
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string samtools_path = "samtools"; |
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|
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bool solexa_quals = false; |
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bool phred64_quals = false; |
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bool quals = false; |
| 148 |
bool integer_quals = false; |
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bool color = false; |
| 150 |
string gtf_juncs = ""; |
| 151 |
|
| 152 |
bool report_secondary_alignments = false; |
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|
| 154 |
string flt_reads = ""; |
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string flt_mappings = ""; |
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|
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bool fusion_search = false; |
| 158 |
size_t fusion_anchor_length = 20; |
| 159 |
size_t fusion_min_dist = 10000000; |
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size_t fusion_read_mismatches = 2; |
| 161 |
size_t fusion_multireads = 2; |
| 162 |
size_t fusion_multipairs = 2; |
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|
| 164 |
eLIBRARY_TYPE library_type = LIBRARY_TYPE_NONE; |
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|
| 166 |
extern void print_usage(); |
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|
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/** |
| 169 |
* Parse an int out of optarg and enforce that it be at least 'lower'; |
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* if it is less than 'lower', than output the given error message and |
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* exit with an error and a usage message. |
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*/ |
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|
| 174 |
int parseIntOpt(int lower, const char *errmsg, void (*print_usage)()) { |
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long l; |
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char *endPtr= NULL; |
| 177 |
l = strtol(optarg, &endPtr, 10); |
| 178 |
if (endPtr != NULL) { |
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if (l < lower) { |
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cerr << errmsg << endl; |
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print_usage(); |
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exit(1); |
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} |
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return (int32_t)l; |
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} |
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cerr << errmsg << endl; |
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print_usage(); |
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exit(1); |
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return -1; |
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} |
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|
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/** |
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* Parse an int out of optarg and enforce that it be at least 'lower'; |
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* if it is less than 'lower', than output the given error message and |
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* exit with an error and a usage message. |
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*/ |
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static float parseFloatOpt(float lower, float upper, const char *errmsg, void (*print_usage)()) { |
| 198 |
float l; |
| 199 |
l = (float)atof(optarg); |
| 200 |
|
| 201 |
if (l < lower) { |
| 202 |
cerr << errmsg << endl; |
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print_usage(); |
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exit(1); |
| 205 |
} |
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|
| 207 |
if (l > upper) |
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{ |
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cerr << errmsg << endl; |
| 210 |
print_usage(); |
| 211 |
exit(1); |
| 212 |
} |
| 213 |
|
| 214 |
return l; |
| 215 |
|
| 216 |
cerr << errmsg << endl; |
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print_usage(); |
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exit(1); |
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return -1; |
| 220 |
} |
| 221 |
|
| 222 |
/* |
| 223 |
this is from |
| 224 |
http://www.winehq.org/pipermail/wine-patches/2001-November/001322.html |
| 225 |
*/ |
| 226 |
char* get_token(char** str, const char* delims) |
| 227 |
{ |
| 228 |
char* token; |
| 229 |
if (*str == NULL) |
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return NULL; |
| 231 |
|
| 232 |
token = *str; |
| 233 |
while (**str != '\0') |
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{ |
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if (strchr(delims, **str) != NULL) |
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{ |
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**str = '\0'; |
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++(*str); |
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return token; |
| 240 |
} |
| 241 |
|
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++(*str); |
| 243 |
} |
| 244 |
|
| 245 |
*str = NULL; |
| 246 |
return token; |
| 247 |
} |
| 248 |
|
| 249 |
const char *short_options = "QCp:z:N:"; |
| 250 |
|
| 251 |
enum |
| 252 |
{ |
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OPT_FASTA = 127, |
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OPT_FASTQ, |
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OPT_MIN_ANCHOR, |
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OPT_SPLICE_MISMATCHES, |
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OPT_VERBOSE, |
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OPT_INSERT_LENGTH_MEAN, |
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OPT_INSERT_LENGTH_STD_DEV, |
| 260 |
OPT_MIN_ISOFORM_FRACTION, |
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OPT_OUTPUT_DIR, |
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OPT_GENE_FILTER, |
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OPT_GFF_ANNOTATIONS, |
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OPT_MAX_MULTIHITS, |
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OPT_MAX_SEG_MULTIHITS, |
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OPT_NO_CLOSURE_SEARCH, |
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OPT_NO_COVERAGE_SEARCH, |
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OPT_NO_MICROEXON_SEARCH, |
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OPT_SEGMENT_LENGTH, |
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OPT_READ_MISMATCHES, |
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OPT_SEGMENT_MISMATCHES, |
| 272 |
OPT_MIN_CLOSURE_EXON, |
| 273 |
OPT_MAX_CLOSURE_INTRON, |
| 274 |
OPT_MIN_CLOSURE_INTRON, |
| 275 |
OPT_MAX_COVERAGE_INTRON, |
| 276 |
OPT_MIN_COVERAGE_INTRON, |
| 277 |
OPT_MIN_SEGMENT_INTRON, |
| 278 |
OPT_MAX_SEGMENT_INTRON, |
| 279 |
OPT_MIN_REPORT_INTRON, |
| 280 |
OPT_MAX_REPORT_INTRON, |
| 281 |
OPT_IUM_READS, |
| 282 |
OPT_BUTTERFLY_SEARCH, |
| 283 |
OPT_SOLEXA_QUALS, |
| 284 |
OPT_PHRED64_QUALS, |
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OPT_SAM_HEADER, |
| 286 |
OPT_SAM_READGROUP_ID, |
| 287 |
OPT_QUALS, |
| 288 |
OPT_INTEGER_QUALS, |
| 289 |
OPT_COLOR, |
| 290 |
OPT_LIBRARY_TYPE, |
| 291 |
OPT_MAX_DELETION_LENGTH, |
| 292 |
OPT_MAX_INSERTION_LENGTH, |
| 293 |
OPT_NUM_THREADS, |
| 294 |
OPT_ZPACKER, |
| 295 |
OPT_SAMTOOLS, |
| 296 |
OPT_AUX_OUT, |
| 297 |
OPT_INDEX_OUT, |
| 298 |
OPT_GTF_JUNCS, |
| 299 |
OPT_FILTER_READS, |
| 300 |
OPT_FILTER_HITS, |
| 301 |
OPT_REPORT_SECONDARY_ALIGNMENTS, |
| 302 |
OPT_FUSION_SEARCH, |
| 303 |
OPT_FUSION_ANCHOR_LENGTH, |
| 304 |
OPT_FUSION_MIN_DIST, |
| 305 |
OPT_FUSION_READ_MISMATCHES, |
| 306 |
OPT_FUSION_MULTIREADS, |
| 307 |
OPT_FUSION_MULTIPAIRS, |
| 308 |
OPT_BOWTIE1, |
| 309 |
OPT_BOWTIE2_MIN_SCORE, |
| 310 |
OPT_BOWTIE2_MAX_PENALTY, |
| 311 |
OPT_BOWTIE2_MIN_PENALTY, |
| 312 |
OPT_BOWTIE2_PENALTY_FOR_N, |
| 313 |
OPT_BOWTIE2_READ_GAP_OPEN, |
| 314 |
OPT_BOWTIE2_READ_GAP_CONT, |
| 315 |
OPT_BOWTIE2_REF_GAP_OPEN, |
| 316 |
OPT_BOWTIE2_REF_GAP_CONT, |
| 317 |
}; |
| 318 |
|
| 319 |
static struct option long_options[] = { |
| 320 |
{"fasta", no_argument, 0, OPT_FASTA}, |
| 321 |
{"fastq", no_argument, 0, OPT_FASTQ}, |
| 322 |
{"min-anchor", required_argument, 0, OPT_MIN_ANCHOR}, |
| 323 |
{"sam-header", required_argument, 0, OPT_SAM_HEADER}, |
| 324 |
{"rg-id", required_argument, 0, OPT_SAM_READGROUP_ID}, |
| 325 |
{"splice-mismatches", required_argument, 0, OPT_SPLICE_MISMATCHES}, |
| 326 |
{"verbose", no_argument, 0, OPT_VERBOSE}, |
| 327 |
{"inner-dist-mean", required_argument, 0, OPT_INSERT_LENGTH_MEAN}, |
| 328 |
{"inner-dist-std-dev", required_argument, 0, OPT_INSERT_LENGTH_STD_DEV}, |
| 329 |
{"output-dir", required_argument, 0, OPT_OUTPUT_DIR}, |
| 330 |
{"gene-filter", required_argument, 0, OPT_GENE_FILTER}, |
| 331 |
{"gtf-annotations", required_argument, 0, OPT_GFF_ANNOTATIONS}, |
| 332 |
{"max-multihits", required_argument, 0, OPT_MAX_MULTIHITS}, |
| 333 |
{"max-seg-multihits", required_argument, 0, OPT_MAX_SEG_MULTIHITS}, |
| 334 |
{"no-closure-search", no_argument, 0, OPT_NO_CLOSURE_SEARCH}, |
| 335 |
{"no-coverage-search", no_argument, 0, OPT_NO_COVERAGE_SEARCH}, |
| 336 |
{"no-microexon-search", no_argument, 0, OPT_NO_MICROEXON_SEARCH}, |
| 337 |
{"segment-length", required_argument, 0, OPT_SEGMENT_LENGTH}, |
| 338 |
{"segment-mismatches", required_argument, 0, OPT_SEGMENT_MISMATCHES}, |
| 339 |
{"max-mismatches", required_argument, 0, OPT_READ_MISMATCHES}, |
| 340 |
{"min-closure-exon", required_argument, 0, OPT_MIN_CLOSURE_EXON}, |
| 341 |
{"min-closure-intron", required_argument, 0, OPT_MIN_CLOSURE_INTRON}, |
| 342 |
{"max-closure-intron", required_argument, 0, OPT_MAX_CLOSURE_INTRON}, |
| 343 |
{"min-coverage-intron", required_argument, 0, OPT_MIN_COVERAGE_INTRON}, |
| 344 |
{"max-coverage-intron", required_argument, 0, OPT_MAX_COVERAGE_INTRON}, |
| 345 |
{"min-segment-intron", required_argument, 0, OPT_MIN_SEGMENT_INTRON}, |
| 346 |
{"max-segment-intron", required_argument, 0, OPT_MAX_SEGMENT_INTRON}, |
| 347 |
{"min-report-intron", required_argument, 0, OPT_MIN_REPORT_INTRON}, |
| 348 |
{"max-report-intron", required_argument, 0, OPT_MAX_REPORT_INTRON}, |
| 349 |
{"min-isoform-fraction",required_argument, 0, OPT_MIN_ISOFORM_FRACTION}, |
| 350 |
{"ium-reads", required_argument, 0, OPT_IUM_READS}, |
| 351 |
{"butterfly-search", no_argument, 0, OPT_BUTTERFLY_SEARCH}, |
| 352 |
{"solexa-quals", no_argument, 0, OPT_SOLEXA_QUALS}, |
| 353 |
{"phred64-quals", no_argument, 0, OPT_PHRED64_QUALS}, |
| 354 |
{"quals", no_argument, 0, OPT_QUALS}, |
| 355 |
{"integer-quals", no_argument, 0, OPT_INTEGER_QUALS}, |
| 356 |
{"color", no_argument, 0, OPT_COLOR}, |
| 357 |
{"library-type", required_argument, 0, OPT_LIBRARY_TYPE}, |
| 358 |
{"max-deletion-length", required_argument, 0, OPT_MAX_DELETION_LENGTH}, |
| 359 |
{"max-insertion-length", required_argument, 0, OPT_MAX_INSERTION_LENGTH}, |
| 360 |
{"num-threads", required_argument, 0, OPT_NUM_THREADS}, |
| 361 |
{"zpacker", required_argument, 0, OPT_ZPACKER}, |
| 362 |
{"samtools", required_argument, 0, OPT_SAMTOOLS}, |
| 363 |
{"aux-outfile", required_argument, 0, OPT_AUX_OUT}, |
| 364 |
{"index-outfile", required_argument, 0, OPT_INDEX_OUT}, |
| 365 |
{"gtf-juncs", required_argument, 0, OPT_GTF_JUNCS}, |
| 366 |
{"flt-reads",required_argument, 0, OPT_FILTER_READS}, |
| 367 |
{"flt-hits",required_argument, 0, OPT_FILTER_HITS}, |
| 368 |
{"report-secondary-alignments", no_argument, 0, OPT_REPORT_SECONDARY_ALIGNMENTS}, |
| 369 |
{"fusion-search", no_argument, 0, OPT_FUSION_SEARCH}, |
| 370 |
{"fusion-anchor-length", required_argument, 0, OPT_FUSION_ANCHOR_LENGTH}, |
| 371 |
{"fusion-min-dist", required_argument, 0, OPT_FUSION_MIN_DIST}, |
| 372 |
{"fusion-read-mismatches", required_argument, 0, OPT_FUSION_READ_MISMATCHES}, |
| 373 |
{"fusion-multireads", required_argument, 0, OPT_FUSION_MULTIREADS}, |
| 374 |
{"fusion-multipairs", required_argument, 0, OPT_FUSION_MULTIPAIRS}, |
| 375 |
{"bowtie1", no_argument, 0, OPT_BOWTIE1}, |
| 376 |
{"bowtie2-min-score", required_argument, 0, OPT_BOWTIE2_MIN_SCORE}, |
| 377 |
{"bowtie2-max-penalty", required_argument, 0, OPT_BOWTIE2_MAX_PENALTY}, |
| 378 |
{"bowtie2-min-penalty", required_argument, 0, OPT_BOWTIE2_MIN_PENALTY}, |
| 379 |
{"bowtie2-penalty-for-N", required_argument, 0, OPT_BOWTIE2_PENALTY_FOR_N}, |
| 380 |
{"bowtie2-read-gap-open", required_argument, 0, OPT_BOWTIE2_READ_GAP_OPEN}, |
| 381 |
{"bowtie2-read-gap-cont", required_argument, 0, OPT_BOWTIE2_READ_GAP_CONT}, |
| 382 |
{"bowtie2-ref-gap-open", required_argument, 0, OPT_BOWTIE2_REF_GAP_OPEN}, |
| 383 |
{"bowtie2-ref-gap-cont", required_argument, 0, OPT_BOWTIE2_REF_GAP_CONT}, |
| 384 |
{0, 0, 0, 0} // terminator |
| 385 |
}; |
| 386 |
|
| 387 |
|
| 388 |
void str_appendInt(string& str, int v) { |
| 389 |
stringstream ss; |
| 390 |
ss << v; |
| 391 |
str.append(ss.str()); |
| 392 |
} |
| 393 |
|
| 394 |
bool str_endsWith(string& str, const char* suffix) { |
| 395 |
if (str.empty() || str.length()<3) return false; |
| 396 |
size_t l=strlen(suffix); |
| 397 |
if (str.length()<=l) return false; |
| 398 |
if (str.rfind(suffix, str.length()-l-1)!=string::npos) return true; |
| 399 |
return false; |
| 400 |
} |
| 401 |
|
| 402 |
int parse_options(int argc, char** argv, void (*print_usage)()) |
| 403 |
{ |
| 404 |
int option_index = 0; |
| 405 |
int next_option; |
| 406 |
do { |
| 407 |
next_option = getopt_long(argc, argv, short_options, long_options, &option_index); |
| 408 |
switch (next_option) { |
| 409 |
case -1: |
| 410 |
break; |
| 411 |
case OPT_FASTA: |
| 412 |
reads_format = FASTA; |
| 413 |
break; |
| 414 |
case OPT_FASTQ: |
| 415 |
reads_format = FASTQ; |
| 416 |
break; |
| 417 |
case OPT_MIN_ANCHOR: |
| 418 |
min_anchor_len = (uint32_t)parseIntOpt(3, "--min-anchor arg must be at least 3", print_usage); |
| 419 |
break; |
| 420 |
case OPT_SPLICE_MISMATCHES: |
| 421 |
max_splice_mismatches = parseIntOpt(0, "--splice-mismatches arg must be at least 0", print_usage); |
| 422 |
break; |
| 423 |
case OPT_VERBOSE: |
| 424 |
verbose = true; |
| 425 |
break; |
| 426 |
case OPT_INSERT_LENGTH_MEAN: |
| 427 |
inner_dist_mean = parseIntOpt(-1024, "--inner-dist-mean arg must be at least -1024", print_usage); |
| 428 |
break; |
| 429 |
case OPT_INSERT_LENGTH_STD_DEV: |
| 430 |
inner_dist_std_dev = parseIntOpt(0, "--inner-dist-std-dev arg must be at least 0", print_usage); |
| 431 |
break; |
| 432 |
case OPT_OUTPUT_DIR: |
| 433 |
output_dir = optarg; |
| 434 |
break; |
| 435 |
case OPT_GENE_FILTER: |
| 436 |
gene_filter = optarg; |
| 437 |
break; |
| 438 |
case OPT_GFF_ANNOTATIONS: |
| 439 |
gff_file = optarg; |
| 440 |
break; |
| 441 |
case OPT_MAX_MULTIHITS: |
| 442 |
max_multihits = parseIntOpt(1, "--max-multihits arg must be at least 1", print_usage); |
| 443 |
break; |
| 444 |
case OPT_MAX_SEG_MULTIHITS: |
| 445 |
max_seg_multihits = parseIntOpt(1, "--max-seg-multihits arg must be at least 1", print_usage); |
| 446 |
break; |
| 447 |
case OPT_NO_CLOSURE_SEARCH: |
| 448 |
no_closure_search = true; |
| 449 |
break; |
| 450 |
case OPT_NO_COVERAGE_SEARCH: |
| 451 |
no_coverage_search = true; |
| 452 |
break; |
| 453 |
case OPT_NO_MICROEXON_SEARCH: |
| 454 |
no_microexon_search = true; |
| 455 |
break; |
| 456 |
case OPT_SEGMENT_LENGTH: |
| 457 |
segment_length = parseIntOpt(4, "--segment-length arg must be at least 4", print_usage); |
| 458 |
break; |
| 459 |
case OPT_SEGMENT_MISMATCHES: |
| 460 |
segment_mismatches = parseIntOpt(0, "--segment-mismatches arg must be at least 0", print_usage); |
| 461 |
break; |
| 462 |
case 'N': |
| 463 |
case OPT_READ_MISMATCHES: |
| 464 |
max_read_mismatches = parseIntOpt(0, "--max-mismatches arg must be at least 0", print_usage); |
| 465 |
break; |
| 466 |
case OPT_MIN_CLOSURE_EXON: |
| 467 |
min_closure_exon_length = parseIntOpt(1, "--min-closure-exon arg must be at least 1", print_usage); |
| 468 |
break; |
| 469 |
case OPT_MIN_CLOSURE_INTRON: |
| 470 |
min_closure_intron_length = parseIntOpt(1, "--min-closure-intron arg must be at least 1", print_usage); |
| 471 |
break; |
| 472 |
case OPT_MAX_CLOSURE_INTRON: |
| 473 |
max_closure_intron_length = parseIntOpt(1, "--max-closure-intron arg must be at least 1", print_usage); |
| 474 |
break; |
| 475 |
case OPT_MIN_COVERAGE_INTRON: |
| 476 |
min_coverage_intron_length = parseIntOpt(1, "--min-coverage-intron arg must be at least 1", print_usage); |
| 477 |
break; |
| 478 |
case OPT_MAX_COVERAGE_INTRON: |
| 479 |
max_coverage_intron_length = parseIntOpt(1, "--max-coverage-intron arg must be at least 1", print_usage); |
| 480 |
break; |
| 481 |
case OPT_MIN_SEGMENT_INTRON: |
| 482 |
min_segment_intron_length = parseIntOpt(1, "--min-segment-intron arg must be at least 1", print_usage); |
| 483 |
break; |
| 484 |
case OPT_MAX_SEGMENT_INTRON: |
| 485 |
max_segment_intron_length = parseIntOpt(1, "--max-segment-intron arg must be at least 1", print_usage); |
| 486 |
break; |
| 487 |
case OPT_MIN_REPORT_INTRON: |
| 488 |
min_report_intron_length = parseIntOpt(1, "--min-report-intron arg must be at least 1", print_usage); |
| 489 |
break; |
| 490 |
case OPT_MAX_REPORT_INTRON: |
| 491 |
max_report_intron_length = parseIntOpt(1, "--max-report-intron arg must be at least 1", print_usage); |
| 492 |
break; |
| 493 |
case OPT_MIN_ISOFORM_FRACTION: |
| 494 |
min_isoform_fraction = parseFloatOpt(0.0f, 1.0f, "--min-isoform-fraction arg must be [0.0,1.0]", print_usage); |
| 495 |
break; |
| 496 |
case OPT_IUM_READS: |
| 497 |
ium_reads = optarg; |
| 498 |
break; |
| 499 |
case OPT_SAM_HEADER: |
| 500 |
sam_header = optarg; |
| 501 |
break; |
| 502 |
case OPT_SAM_READGROUP_ID: |
| 503 |
sam_readgroup_id = optarg; |
| 504 |
break; |
| 505 |
case OPT_BUTTERFLY_SEARCH: |
| 506 |
butterfly_search = true; |
| 507 |
break; |
| 508 |
case OPT_SOLEXA_QUALS: |
| 509 |
solexa_quals = true; |
| 510 |
break; |
| 511 |
case OPT_PHRED64_QUALS: |
| 512 |
phred64_quals = true; |
| 513 |
break; |
| 514 |
case 'Q': |
| 515 |
case OPT_QUALS: |
| 516 |
quals = true; |
| 517 |
break; |
| 518 |
case OPT_INTEGER_QUALS: |
| 519 |
integer_quals = true; |
| 520 |
break; |
| 521 |
case 'C': |
| 522 |
case OPT_COLOR: |
| 523 |
color = true; |
| 524 |
break; |
| 525 |
case OPT_LIBRARY_TYPE: |
| 526 |
if (strcmp(optarg, "fr-unstranded") == 0) |
| 527 |
library_type = FR_UNSTRANDED; |
| 528 |
else if (strcmp(optarg, "fr-firststrand") == 0) |
| 529 |
library_type = FR_FIRSTSTRAND; |
| 530 |
else if (strcmp(optarg, "fr-secondstrand") == 0) |
| 531 |
library_type = FR_SECONDSTRAND; |
| 532 |
else if (strcmp(optarg, "ff-unstranded") == 0) |
| 533 |
library_type = FF_UNSTRANDED; |
| 534 |
else if (strcmp(optarg, "ff-firststrand") == 0) |
| 535 |
library_type = FF_FIRSTSTRAND; |
| 536 |
else if (strcmp(optarg, "ff-secondstrand") == 0) |
| 537 |
library_type = FF_SECONDSTRAND; |
| 538 |
break; |
| 539 |
case OPT_MAX_DELETION_LENGTH: |
| 540 |
max_deletion_length = parseIntOpt(0, "--max-deletion-length must be at least 0", print_usage); |
| 541 |
break; |
| 542 |
case OPT_MAX_INSERTION_LENGTH: |
| 543 |
max_insertion_length = parseIntOpt(0, "--max-insertion-length must be at least 0", print_usage); |
| 544 |
break; |
| 545 |
case 'z': |
| 546 |
case OPT_ZPACKER: |
| 547 |
zpacker = optarg; |
| 548 |
break; |
| 549 |
case OPT_SAMTOOLS: |
| 550 |
samtools_path = optarg; |
| 551 |
break; |
| 552 |
case OPT_AUX_OUT: |
| 553 |
aux_outfile = optarg; |
| 554 |
break; |
| 555 |
case OPT_INDEX_OUT: |
| 556 |
index_outfile = optarg; |
| 557 |
break; |
| 558 |
case 'p': |
| 559 |
case OPT_NUM_THREADS: |
| 560 |
num_threads=parseIntOpt(1,"-p/--num-threads must be at least 1",print_usage); |
| 561 |
break; |
| 562 |
case OPT_GTF_JUNCS: |
| 563 |
gtf_juncs = optarg; |
| 564 |
break; |
| 565 |
case OPT_FILTER_READS: |
| 566 |
flt_reads = optarg; |
| 567 |
break; |
| 568 |
case OPT_FILTER_HITS: |
| 569 |
flt_mappings = optarg; |
| 570 |
break; |
| 571 |
case OPT_REPORT_SECONDARY_ALIGNMENTS: |
| 572 |
report_secondary_alignments = true; |
| 573 |
break; |
| 574 |
case OPT_FUSION_SEARCH: |
| 575 |
fusion_search = true; |
| 576 |
break; |
| 577 |
case OPT_FUSION_ANCHOR_LENGTH: |
| 578 |
fusion_anchor_length = parseIntOpt(10, "--fusion-anchor-length must be at least 10", print_usage); |
| 579 |
break; |
| 580 |
case OPT_FUSION_MIN_DIST: |
| 581 |
fusion_min_dist = parseIntOpt(0, "--fusion-min-dist must be at least 0", print_usage); |
| 582 |
break; |
| 583 |
case OPT_FUSION_READ_MISMATCHES: |
| 584 |
fusion_read_mismatches = parseIntOpt(0, "--fusion-read-mismatches must be at least 0", print_usage); |
| 585 |
break; |
| 586 |
case OPT_FUSION_MULTIREADS: |
| 587 |
fusion_multireads = parseIntOpt(1, "--fusion-multireads must be at least 1", print_usage); |
| 588 |
break; |
| 589 |
case OPT_FUSION_MULTIPAIRS: |
| 590 |
fusion_multipairs = parseIntOpt(1, "--fusion-multipairs must be at least 0", print_usage); |
| 591 |
break; |
| 592 |
case OPT_BOWTIE1: |
| 593 |
bowtie2 = false; |
| 594 |
break; |
| 595 |
case OPT_BOWTIE2_MIN_SCORE: |
| 596 |
bowtie2_min_score = -1 * parseIntOpt(0, "--bowtie2-min-score must be at least 0", print_usage); |
| 597 |
break; |
| 598 |
case OPT_BOWTIE2_MAX_PENALTY: |
| 599 |
bowtie2_max_penalty = parseIntOpt(0, "--bowtie2-max-penalty must be at least 0", print_usage); |
| 600 |
break; |
| 601 |
case OPT_BOWTIE2_MIN_PENALTY: |
| 602 |
bowtie2_min_penalty = parseIntOpt(0, "--bowtie2-min-penalty must be at least 0", print_usage); |
| 603 |
break; |
| 604 |
case OPT_BOWTIE2_PENALTY_FOR_N: |
| 605 |
bowtie2_penalty_for_N = parseIntOpt(0, "--bowtie2-penalty-for-N must be at least 0", print_usage); |
| 606 |
break; |
| 607 |
case OPT_BOWTIE2_READ_GAP_OPEN: |
| 608 |
bowtie2_read_gap_open = parseIntOpt(0, "--bowtie2-read-gap-open must be at least 0", print_usage); |
| 609 |
break; |
| 610 |
case OPT_BOWTIE2_READ_GAP_CONT: |
| 611 |
bowtie2_read_gap_cont = parseIntOpt(0, "--bowtie2-read-gap-cont must be at least 0", print_usage); |
| 612 |
break; |
| 613 |
case OPT_BOWTIE2_REF_GAP_OPEN: |
| 614 |
bowtie2_ref_gap_open = parseIntOpt(0, "--bowtie2-ref-gap-open must be at least 0", print_usage); |
| 615 |
break; |
| 616 |
case OPT_BOWTIE2_REF_GAP_CONT: |
| 617 |
bowtie2_ref_gap_cont = parseIntOpt(0, "--bowtie2-ref-gap-cont must be at least 0", print_usage); |
| 618 |
break; |
| 619 |
default: |
| 620 |
print_usage(); |
| 621 |
return 1; |
| 622 |
} |
| 623 |
} while(next_option != -1); |
| 624 |
|
| 625 |
return 0; |
| 626 |
} |
| 627 |
|
| 628 |
|
| 629 |
// Error routine (prints error message and exits!) |
| 630 |
void err_exit(const char* format,...){ |
| 631 |
va_list arguments; |
| 632 |
va_start(arguments,format); |
| 633 |
vfprintf(stderr,format,arguments); |
| 634 |
va_end(arguments); |
| 635 |
#ifdef DEBUG |
| 636 |
// trigger a core dump for later inspection |
| 637 |
abort(); |
| 638 |
#endif |
| 639 |
exit(1); |
| 640 |
} |
| 641 |
|
| 642 |
FILE* FZPipe::openRead(const char* fname, string& popencmd) { |
| 643 |
pipecmd=popencmd; |
| 644 |
filename=fname; |
| 645 |
if (pipecmd.empty()) { |
| 646 |
file=fopen(filename.c_str(), "r"); |
| 647 |
} |
| 648 |
else { |
| 649 |
string pcmd(pipecmd); |
| 650 |
pcmd.append(" '"); |
| 651 |
pcmd.append(filename); |
| 652 |
pcmd.append("'"); |
| 653 |
file=popen(pcmd.c_str(), "r"); |
| 654 |
} |
| 655 |
return file; |
| 656 |
} |
| 657 |
|
| 658 |
FILE* FZPipe::openRead(const char* fname) { |
| 659 |
string pcmd; |
| 660 |
return this->openRead(fname,pcmd); |
| 661 |
} |
| 662 |
|
| 663 |
FILE* FZPipe::openWrite(const char* fname, string& popencmd) { |
| 664 |
pipecmd=popencmd; |
| 665 |
filename=fname; |
| 666 |
if (pipecmd.empty()) { |
| 667 |
file=fopen(filename.c_str(), "w"); |
| 668 |
} |
| 669 |
else { |
| 670 |
string pcmd(pipecmd); |
| 671 |
pcmd.append(" - > '"); |
| 672 |
pcmd.append(filename.c_str()); |
| 673 |
pcmd.append("'"); |
| 674 |
file=popen(pcmd.c_str(), "w"); |
| 675 |
} |
| 676 |
return file; |
| 677 |
} |
| 678 |
|
| 679 |
|
| 680 |
FILE* FZPipe::openWrite(const char* fname) { |
| 681 |
string pcmd; |
| 682 |
return this->openWrite(fname,pcmd); |
| 683 |
} |
| 684 |
|
| 685 |
void FZPipe::rewind() { |
| 686 |
if (pipecmd.empty()) { |
| 687 |
if (file!=NULL) { |
| 688 |
::rewind(file); |
| 689 |
return; |
| 690 |
} |
| 691 |
if (!filename.empty()) { |
| 692 |
file=fopen(filename.c_str(),"r"); |
| 693 |
return; |
| 694 |
} |
| 695 |
} |
| 696 |
if (filename.empty()) |
| 697 |
err_die("Error: FZStream::rewind() failed (missing filename)!\n"); |
| 698 |
this->close(); |
| 699 |
string pcmd(pipecmd); |
| 700 |
pcmd.append(" '"); |
| 701 |
pcmd.append(filename); |
| 702 |
pcmd.append("'"); |
| 703 |
file=popen(pcmd.c_str(), "r"); |
| 704 |
if (file==NULL) { |
| 705 |
err_die("Error: FZStream::rewind() popen(%s) failed!\n",pcmd.c_str()); |
| 706 |
} |
| 707 |
} |
| 708 |
|
| 709 |
|
| 710 |
string getFext(const string& s) { |
| 711 |
string r(""); |
| 712 |
//if (xpos!=NULL) *xpos=0; |
| 713 |
if (s.empty() || s=="-") return r; |
| 714 |
int slen=(int)s.length(); |
| 715 |
int p=s.rfind('.'); |
| 716 |
int d=s.rfind('/'); |
| 717 |
if (p<=0 || p>slen-2 || p<slen-7 || p<d) return r; |
| 718 |
r=s.substr(p+1); |
| 719 |
//if (xpos!=NULL) *xpos=p+1; |
| 720 |
for(size_t i=0; i!=r.length(); i++) |
| 721 |
r[i] = std::tolower(r[i]); |
| 722 |
return r; |
| 723 |
} |
| 724 |
|
| 725 |
string guess_packer(const string& fname, bool use_all_cpus) { |
| 726 |
//only needed for the primary input files (given by user) |
| 727 |
string picmd(""); |
| 728 |
string fext=getFext(fname); |
| 729 |
if (fext=="bam") { |
| 730 |
picmd="bam2fastx"; |
| 731 |
return picmd; |
| 732 |
} |
| 733 |
if (fext=="gz" || fext=="gzip" || fext=="z") { |
| 734 |
if (use_all_cpus && str_endsWith(zpacker,"pigz")) { |
| 735 |
picmd=zpacker; |
| 736 |
if (num_threads<2) picmd.append(" -p1"); |
| 737 |
else { |
| 738 |
picmd.append(" -p"); |
| 739 |
str_appendInt(picmd, num_threads); |
| 740 |
//picmd.append(" -cd"); |
| 741 |
} |
| 742 |
} |
| 743 |
else picmd="gzip"; |
| 744 |
} |
| 745 |
else if (fext=="bz2" || fext=="bzip2" || fext=="bz" || fext=="bzip") { |
| 746 |
if (use_all_cpus && str_endsWith(zpacker,"pbzip2")) { |
| 747 |
picmd=zpacker; |
| 748 |
if (num_threads<2) picmd.append(" -p1"); |
| 749 |
else { |
| 750 |
picmd.append(" -p"); |
| 751 |
str_appendInt(picmd, num_threads); |
| 752 |
//picmd.append(" -cd"); |
| 753 |
} |
| 754 |
} |
| 755 |
else picmd="bzip2"; |
| 756 |
} |
| 757 |
return picmd; |
| 758 |
} |
| 759 |
|
| 760 |
/* |
| 761 |
string getBam2SamCmd(const string& fname) { |
| 762 |
string pipecmd(""); |
| 763 |
string fext=getFext(fname); |
| 764 |
if (fext=="bam") { |
| 765 |
pipecmd=samtools_path; |
| 766 |
pipecmd.append(" view"); |
| 767 |
} |
| 768 |
return pipecmd; |
| 769 |
} |
| 770 |
*/ |
| 771 |
|
| 772 |
void err_die(const char* format,...) { // Error exit |
| 773 |
va_list arguments; |
| 774 |
va_start(arguments,format); |
| 775 |
vfprintf(stderr,format,arguments); |
| 776 |
va_end(arguments); |
| 777 |
exit(1); |
| 778 |
} |
| 779 |
|
| 780 |
string getUnpackCmd(const string& fname, bool use_all_cpus) { |
| 781 |
//prep_reads should use guess_packer() instead |
| 782 |
//otherwise compressed files MUST have the .z extension, |
| 783 |
//as they are all internally generated |
| 784 |
string pipecmd(""); |
| 785 |
string fext=getFext(fname); |
| 786 |
if (fext=="bam") { |
| 787 |
pipecmd="bam2fastx"; |
| 788 |
return pipecmd; |
| 789 |
} |
| 790 |
if (zpacker.empty() || fext!="z") { |
| 791 |
return pipecmd; //no packer used |
| 792 |
} |
| 793 |
pipecmd=zpacker; |
| 794 |
if (str_endsWith(pipecmd, "pigz") ||str_endsWith(pipecmd, "pbzip2")) { |
| 795 |
if (use_all_cpus==false) pipecmd.append(" -p1"); |
| 796 |
else if (num_threads>1) { |
| 797 |
pipecmd.append(" -p"); |
| 798 |
str_appendInt(pipecmd,num_threads); |
| 799 |
} |
| 800 |
} |
| 801 |
if (!pipecmd.empty()) pipecmd.append(" -cd"); |
| 802 |
return pipecmd; |
| 803 |
} |
| 804 |
|
| 805 |
void checkSamHeader() { |
| 806 |
if (sam_header.empty()) |
| 807 |
err_die("Error: writeSamHeader() with empty sam_header string\n"); |
| 808 |
//copy the SAM header |
| 809 |
FILE* fh=fopen(sam_header.c_str(), "r"); |
| 810 |
if (fh==NULL) |
| 811 |
err_die("Error: cannot open SAM header file %s\n",sam_header.c_str()); |
| 812 |
fclose(fh); |
| 813 |
} |
| 814 |
|
| 815 |
void writeSamHeader(FILE* fout) { |
| 816 |
if (fout==NULL) |
| 817 |
err_die("Error: writeSamHeader(NULL)\n"); |
| 818 |
checkSamHeader(); |
| 819 |
//copy the SAM header |
| 820 |
FILE* fh=fopen(sam_header.c_str(), "r"); |
| 821 |
int ch=-1; |
| 822 |
while ((ch=fgetc(fh))!=EOF) { |
| 823 |
if (fputc(ch, fout)==EOF) |
| 824 |
err_die("Error copying SAM header\n"); |
| 825 |
} |
| 826 |
fclose(fh); |
| 827 |
} |
| 828 |
|
| 829 |
//auxiliary functions for BAM record handling |
| 830 |
uint8_t* realloc_bdata(bam1_t *b, int size) { |
| 831 |
if (b->m_data < size) { |
| 832 |
b->m_data = size; |
| 833 |
kroundup32(b->m_data); |
| 834 |
b->data = (uint8_t*)realloc(b->data, b->m_data); |
| 835 |
} |
| 836 |
if (b->data_len<size) b->data_len=size; |
| 837 |
return b->data; |
| 838 |
} |
| 839 |
|
| 840 |
uint8_t* dupalloc_bdata(bam1_t *b, int size) { |
| 841 |
//same as realloc_bdata, but does not free previous data |
| 842 |
//but returns it instead |
| 843 |
//it ALWAYS duplicates data |
| 844 |
b->m_data = size; |
| 845 |
kroundup32(b->m_data); |
| 846 |
uint8_t* odata=b->data; |
| 847 |
b->data = (uint8_t*)malloc(b->m_data); |
| 848 |
memcpy((void*)b->data, (void*)odata, b->data_len); |
| 849 |
b->data_len=size; |
| 850 |
return odata; //user must FREE this after |
| 851 |
} |
| 852 |
|
| 853 |
extern unsigned short bam_char2flag_table[]; |
| 854 |
|
| 855 |
GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid, |
| 856 |
int pos, bool reverse, const char* qseq, const char* cigar, const char* quals) { |
| 857 |
novel=true; |
| 858 |
b=bam_init1(); |
| 859 |
b->core.tid=gseq_tid; |
| 860 |
if (pos<=0) { |
| 861 |
b->core.pos=-1; //unmapped |
| 862 |
//if (gseq_tid<0) |
| 863 |
b->core.flag |= BAM_FUNMAP; |
| 864 |
} |
| 865 |
else b->core.pos=pos-1; //BAM is 0-based |
| 866 |
b->core.qual=255; |
| 867 |
int l_qseq=strlen(qseq); |
| 868 |
//this may not be accurate, setting CIGAR is the correct way |
| 869 |
//b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1); |
| 870 |
b->core.l_qname=strlen(qname)+1; //includes the \0 at the end |
| 871 |
memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname); |
| 872 |
set_cigar(cigar); //this will also set core.bin |
| 873 |
add_sequence(qseq, l_qseq); |
| 874 |
add_quals(quals); //quals must be given as Phred33 |
| 875 |
if (reverse) { b->core.flag |= BAM_FREVERSE ; } |
| 876 |
} |
| 877 |
|
| 878 |
GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid, |
| 879 |
int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos, |
| 880 |
int insert_size, const char* qseq, const char* quals, |
| 881 |
const vector<string>* aux_strings) { |
| 882 |
novel=true; |
| 883 |
b=bam_init1(); |
| 884 |
b->core.tid=g_tid; |
| 885 |
b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based |
| 886 |
b->core.qual=map_qual; |
| 887 |
int l_qseq=strlen(qseq); |
| 888 |
b->core.l_qname=strlen(qname)+1; //includes the \0 at the end |
| 889 |
memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname); |
| 890 |
set_cigar(cigar); //this will also set core.bin |
| 891 |
add_sequence(qseq, l_qseq); |
| 892 |
add_quals(quals); //quals must be given as Phred33 |
| 893 |
set_flags(flags); |
| 894 |
set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size); |
| 895 |
if (aux_strings!=NULL) { |
| 896 |
for (vector<string>::const_iterator itr=aux_strings->begin(); |
| 897 |
itr!=aux_strings->end(); ++itr) { |
| 898 |
add_aux(itr->c_str()); |
| 899 |
} |
| 900 |
} |
| 901 |
} |
| 902 |
void GBamRecord::set_cigar(const char* cigar) { |
| 903 |
//requires b->core.pos and b->core.flag to have been set properly PRIOR to this call |
| 904 |
int doff=b->core.l_qname; |
| 905 |
uint8_t* after_cigar=NULL; |
| 906 |
int after_cigar_len=0; |
| 907 |
uint8_t* prev_bdata=NULL; |
| 908 |
if (b->data_len>doff) { |
| 909 |
//cigar string already allocated, replace it |
| 910 |
int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data |
| 911 |
after_cigar=b->data+d; |
| 912 |
after_cigar_len=b->data_len-d; |
| 913 |
} |
| 914 |
const char *s; |
| 915 |
char *t; |
| 916 |
int i, op; |
| 917 |
long x; |
| 918 |
b->core.n_cigar = 0; |
| 919 |
if (cigar != NULL && strcmp(cigar, "*") != 0) { |
| 920 |
for (s = cigar; *s; ++s) { |
| 921 |
if (isalpha(*s)) b->core.n_cigar++; |
| 922 |
else if (!isdigit(*s)) { |
| 923 |
err_die("Error: invalid CIGAR character (%s)\n",cigar); |
| 924 |
} |
| 925 |
} |
| 926 |
if (after_cigar_len>0) { //replace/insert into existing full data |
| 927 |
prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len); |
| 928 |
memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len); |
| 929 |
free(prev_bdata); |
| 930 |
} |
| 931 |
else { |
| 932 |
realloc_bdata(b, doff + b->core.n_cigar * 4); |
| 933 |
} |
| 934 |
for (i = 0, s = cigar; i != (int)b->core.n_cigar; ++i) { |
| 935 |
x = strtol(s, &t, 10); |
| 936 |
op = toupper(*t); |
| 937 |
if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH; |
| 938 |
else if (op == 'I') op = BAM_CINS; |
| 939 |
else if (op == 'D') op = BAM_CDEL; |
| 940 |
else if (op == 'N') op = BAM_CREF_SKIP; |
| 941 |
else if (op == 'S') op = BAM_CSOFT_CLIP; |
| 942 |
else if (op == 'H') op = BAM_CHARD_CLIP; |
| 943 |
else if (op == 'P') op = BAM_CPAD; |
| 944 |
else err_die("Error: invalid CIGAR operation (%s)\n",cigar); |
| 945 |
s = t + 1; |
| 946 |
bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op; |
| 947 |
} |
| 948 |
if (*s) err_die("Error: unmatched CIGAR operation (%s)\n",cigar); |
| 949 |
b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b))); |
| 950 |
} else {//no CIGAR string given |
| 951 |
if (!(b->core.flag&BAM_FUNMAP)) { |
| 952 |
fprintf(stderr, "Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data); |
| 953 |
b->core.flag |= BAM_FUNMAP; |
| 954 |
} |
| 955 |
b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1); |
| 956 |
} |
| 957 |
} //set_cigar() |
| 958 |
|
| 959 |
void GBamRecord::add_sequence(const char* qseq, int slen) { |
| 960 |
//must be called AFTER set_cigar (cannot replace existing sequence for now) |
| 961 |
if (qseq==NULL) return; //should we ever care about this? |
| 962 |
if (slen<0) slen=strlen(qseq); |
| 963 |
int doff = b->core.l_qname + b->core.n_cigar * 4; |
| 964 |
if (strcmp(qseq, "*")!=0) { |
| 965 |
b->core.l_qseq=slen; |
| 966 |
if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b))) |
| 967 |
err_die("Error: CIGAR and sequence length are inconsistent!(%s)\n", |
| 968 |
qseq); |
| 969 |
uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff; |
| 970 |
//also allocated quals memory |
| 971 |
memset(p, 0, (b->core.l_qseq+1)/2); |
| 972 |
for (int i = 0; i < b->core.l_qseq; ++i) |
| 973 |
p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2); |
| 974 |
} else b->core.l_qseq = 0; |
| 975 |
} |
| 976 |
|
| 977 |
void GBamRecord::add_quals(const char* quals) { |
| 978 |
//requires core.l_qseq already set |
| 979 |
//and must be called AFTER add_sequence(), which also allocates the memory for quals |
| 980 |
uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2); |
| 981 |
if (quals==NULL || strcmp(quals, "*") == 0) { |
| 982 |
for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff; |
| 983 |
return; |
| 984 |
} |
| 985 |
for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33; |
| 986 |
} |
| 987 |
|
| 988 |
void GBamRecord::add_aux(const char* str) { |
| 989 |
//requires: being called AFTER add_quals() |
| 990 |
// static char tag[2]; |
| 991 |
// static uint8_t abuf[512]; |
| 992 |
//requires: being called AFTER add_quals() |
| 993 |
int strl=strlen(str); |
| 994 |
//int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux; |
| 995 |
//int doff0=doff; |
| 996 |
if (strl < 6 || str[2] != ':' || str[4] != ':') |
| 997 |
parse_error("missing colon in auxiliary data"); |
| 998 |
tag[0] = str[0]; tag[1] = str[1]; |
| 999 |
uint8_t atype = str[3]; |
| 1000 |
uint8_t* adata=abuf; |
| 1001 |
int alen=0; |
| 1002 |
if (atype == 'A' || atype == 'a' || atype == 'c' || atype == 'C') { // c and C for backward compatibility |
| 1003 |
atype='A'; |
| 1004 |
alen=1; |
| 1005 |
adata=(uint8_t*)&str[5]; |
| 1006 |
} |
| 1007 |
else if (atype == 'I' || atype == 'i') { |
| 1008 |
long long x=(long long)atoll(str + 5); |
| 1009 |
if (x < 0) { |
| 1010 |
if (x >= -127) { |
| 1011 |
atype='c'; |
| 1012 |
abuf[0] = (int8_t)x; |
| 1013 |
alen=1; |
| 1014 |
} |
| 1015 |
else if (x >= -32767) { |
| 1016 |
atype = 's'; |
| 1017 |
*(int16_t*)abuf = (int16_t)x; |
| 1018 |
alen=2; |
| 1019 |
} |
| 1020 |
else { |
| 1021 |
atype='i'; |
| 1022 |
*(int32_t*)abuf = (int32_t)x; |
| 1023 |
alen=4; |
| 1024 |
if (x < -2147483648ll) |
| 1025 |
fprintf(stderr, "Parse warning: integer %lld is out of range.", |
| 1026 |
x); |
| 1027 |
} |
| 1028 |
} else { //x >=0 |
| 1029 |
if (x <= 255) { |
| 1030 |
atype = 'C'; |
| 1031 |
abuf[0] = (uint8_t)x; |
| 1032 |
alen=1; |
| 1033 |
} |
| 1034 |
else if (x <= 65535) { |
| 1035 |
atype='S'; |
| 1036 |
*(uint16_t*)abuf = (uint16_t)x; |
| 1037 |
alen=2; |
| 1038 |
} |
| 1039 |
else { |
| 1040 |
atype='I'; |
| 1041 |
*(uint32_t*)abuf = (uint32_t)x; |
| 1042 |
alen=4; |
| 1043 |
if (x > 4294967295ll) |
| 1044 |
fprintf(stderr, "Parse warning: integer %lld is out of range.", |
| 1045 |
x); |
| 1046 |
} |
| 1047 |
} |
| 1048 |
} //integer type |
| 1049 |
else if (atype == 'f') { |
| 1050 |
*(float*)abuf = (float)atof(str + 5); |
| 1051 |
alen = sizeof(float); |
| 1052 |
} |
| 1053 |
else if (atype == 'd') { //? |
| 1054 |
*(float*)abuf = (float)atof(str + 9); |
| 1055 |
alen=8; |
| 1056 |
} |
| 1057 |
else if (atype == 'Z' || atype == 'H') { |
| 1058 |
if (atype == 'H') { // check whether the hex string is valid |
| 1059 |
if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even"); |
| 1060 |
for (int i = 0; i < strl - 5; ++i) { |
| 1061 |
int c = toupper(str[5 + i]); |
| 1062 |
if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F'))) |
| 1063 |
parse_error("invalid hex character"); |
| 1064 |
} |
| 1065 |
} |
| 1066 |
memcpy(abuf, str + 5, strl - 5); |
| 1067 |
abuf[strl-5] = 0; |
| 1068 |
alen=strl-4; |
| 1069 |
} else parse_error("unrecognized aux type"); |
| 1070 |
this->add_aux(tag, atype, alen, adata); |
| 1071 |
}//add_aux() |
