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root/gclib/tophat_cpp/common.cpp
Revision: 32
Committed: Tue Aug 2 22:04:47 2011 UTC (9 years, 6 months ago) by gpertea
File size: 29376 byte(s)
Log Message:
adding bam2fastx as recognized unpacker for .bam files

Line User Rev File contents
1 gpertea 29 /*
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 <getopt.h>
18    
19     #include "common.h"
20    
21     using namespace std;
22    
23     #ifdef MEM_DEBUG
24     //function for debugging memory usage of current program in Linux
25    
26     #include <unistd.h>
27     #include <ios>
28     #include <fstream>
29    
30     //////////////////////////////////////////////////////////////////////////////
31     // process_mem_usage(double &, double &) - takes two doubles by reference,
32     // attempts to read the system-dependent data for a process' virtual memory
33     // size and resident set size, and return the results in KB.
34     //
35     // On failure, returns 0.0, 0.0
36    
37     void process_mem_usage(double& vm_usage, double& resident_set) {
38     using std::ios_base;
39     using std::ifstream;
40     using std::string;
41     vm_usage = 0.0;
42     resident_set = 0.0;
43     // 'file' stat seems to give the most reliable results
44     ifstream stat_stream("/proc/self/stat",ios_base::in);
45     // dummy vars for leading entries in stat that we don't care about
46     string pid, comm, state, ppid, pgrp, session, tty_nr;
47     string tpgid, flags, minflt, cminflt, majflt, cmajflt;
48     string utime, stime, cutime, cstime, priority, nice;
49     string O, itrealvalue, starttime;
50    
51     // the two fields we want
52     //
53     unsigned long vsize;
54     long rss;
55    
56     stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
57     >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
58     >> utime >> stime >> cutime >> cstime >> priority >> nice
59     >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
60    
61     stat_stream.close();
62    
63     long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
64     vm_usage = vsize / 1024.0;
65     resident_set = rss * page_size_kb;
66     }
67    
68     void print_mem_usage() {
69     double vs, rs;
70     process_mem_usage(vs,rs);
71     vs/=1024;
72     rs/=1024;
73     fprintf(stderr, "VMSize: %6.1fMB\tRSize: %6.1fMB\n", vs, rs);
74     }
75     #endif
76    
77    
78     unsigned int max_insertion_length = 3;
79     unsigned int max_deletion_length = 3;
80    
81    
82     int inner_dist_mean = 200;
83     int inner_dist_std_dev = 20;
84     int max_mate_inner_dist = -1;
85    
86     int min_anchor_len = 8;
87     int min_report_intron_length = 50;
88     int max_report_intron_length = 500000;
89    
90     int min_closure_intron_length = 50;
91     int max_closure_intron_length = 5000;
92    
93     int min_coverage_intron_length = 50;
94     int max_coverage_intron_length = 20000;
95    
96     int min_segment_intron_length = 50;
97     int max_segment_intron_length = 500000;
98    
99     uint32_t min_closure_exon_length = 100;
100    
101     int island_extension = 25;
102     int segment_length = 25;
103     int segment_mismatches = 2;
104    
105     int max_splice_mismatches = 1;
106    
107     ReadFormat reads_format = FASTQ;
108    
109     bool verbose = false;
110    
111     int max_multihits = 40;
112     bool no_closure_search = false;
113     bool no_coverage_search = false;
114     bool no_microexon_search = false;
115     bool butterfly_search = false;
116     int num_cpus = 1;
117     float min_isoform_fraction = 0.15f;
118    
119     string output_dir = "tophat_out";
120     string aux_outfile = ""; //auxiliary output file name (e.g. prep_reads read stats)
121     string gene_filter = "";
122     string gff_file = "";
123     string ium_reads = "";
124     string sam_header = "";
125     string sam_readgroup_id = "";
126     string zpacker = "";
127     string samtools_path = "samtools";
128    
129     bool solexa_quals = false;
130     bool phred64_quals = false;
131     bool quals = false;
132     bool integer_quals = false;
133     bool color = false;
134     bool color_out = false;
135    
136     string gtf_juncs = "";
137    
138     eLIBRARY_TYPE library_type = LIBRARY_TYPE_NONE;
139    
140     extern void print_usage();
141    
142     /**
143     * Parse an int out of optarg and enforce that it be at least 'lower';
144     * if it is less than 'lower', than output the given error message and
145     * exit with an error and a usage message.
146     */
147    
148     int parseIntOpt(int lower, const char *errmsg, void (*print_usage)()) {
149     long l;
150     char *endPtr= NULL;
151     l = strtol(optarg, &endPtr, 10);
152     if (endPtr != NULL) {
153     if (l < lower) {
154     cerr << errmsg << endl;
155     print_usage();
156     exit(1);
157     }
158     return (int32_t)l;
159     }
160     cerr << errmsg << endl;
161     print_usage();
162     exit(1);
163     return -1;
164     }
165    
166     /**
167     * Parse an int out of optarg and enforce that it be at least 'lower';
168     * if it is less than 'lower', than output the given error message and
169     * exit with an error and a usage message.
170     */
171     static float parseFloatOpt(float lower, float upper, const char *errmsg, void (*print_usage)()) {
172     float l;
173     l = (float)atof(optarg);
174    
175     if (l < lower) {
176     cerr << errmsg << endl;
177     print_usage();
178     exit(1);
179     }
180    
181     if (l > upper)
182     {
183     cerr << errmsg << endl;
184     print_usage();
185     exit(1);
186     }
187    
188     return l;
189    
190     cerr << errmsg << endl;
191     print_usage();
192     exit(1);
193     return -1;
194     }
195    
196     /*
197     this is from
198     http://www.winehq.org/pipermail/wine-patches/2001-November/001322.html
199     */
200     char* get_token(char** str, const char* delims)
201     {
202     char* token;
203     if (*str == NULL)
204     return NULL;
205    
206     token = *str;
207     while (**str != '\0')
208     {
209     if (strchr(delims, **str) != NULL)
210     {
211     **str = '\0';
212     ++(*str);
213     return token;
214     }
215    
216     ++(*str);
217     }
218    
219     *str = NULL;
220     return token;
221     }
222    
223    
224     const char *short_options = "QCp:z:";
225    
226     enum
227     {
228     OPT_FASTA = 127,
229     OPT_FASTQ,
230     OPT_MIN_ANCHOR,
231     OPT_SPLICE_MISMATCHES,
232     OPT_VERBOSE,
233     OPT_INSERT_LENGTH_MEAN,
234     OPT_INSERT_LENGTH_STD_DEV,
235     OPT_MIN_ISOFORM_FRACTION,
236     OPT_OUTPUT_DIR,
237     OPT_GENE_FILTER,
238     OPT_GFF_ANNOTATIONS,
239     OPT_MAX_MULTIHITS,
240     OPT_NO_CLOSURE_SEARCH,
241     OPT_NO_COVERAGE_SEARCH,
242     OPT_NO_MICROEXON_SEARCH,
243     OPT_SEGMENT_LENGTH,
244     OPT_SEGMENT_MISMATCHES,
245     OPT_MIN_CLOSURE_EXON,
246     OPT_MAX_CLOSURE_INTRON,
247     OPT_MIN_CLOSURE_INTRON,
248     OPT_MAX_COVERAGE_INTRON,
249     OPT_MIN_COVERAGE_INTRON,
250     OPT_MIN_SEGMENT_INTRON,
251     OPT_MAX_SEGMENT_INTRON,
252     OPT_MIN_REPORT_INTRON,
253     OPT_MAX_REPORT_INTRON,
254     OPT_IUM_READS,
255     OPT_BUTTERFLY_SEARCH,
256     OPT_SOLEXA_QUALS,
257     OPT_PHRED64_QUALS,
258     OPT_SAM_HEADER,
259     OPT_SAM_READGROUP_ID,
260     OPT_QUALS,
261     OPT_INTEGER_QUALS,
262     OPT_COLOR,
263     OPT_COLOR_OUT,
264     OPT_LIBRARY_TYPE,
265     OPT_MAX_DELETION_LENGTH,
266     OPT_MAX_INSERTION_LENGTH,
267     OPT_NUM_CPUS,
268     OPT_ZPACKER,
269     OPT_SAMTOOLS,
270     OPT_AUX_OUT,
271     OPT_GTF_JUNCS
272     };
273    
274     static struct option long_options[] = {
275     {"fasta", no_argument, 0, OPT_FASTA},
276     {"fastq", no_argument, 0, OPT_FASTQ},
277     {"min-anchor", required_argument, 0, OPT_MIN_ANCHOR},
278     {"sam-header", required_argument, 0, OPT_SAM_HEADER},
279     {"rg-id", required_argument, 0, OPT_SAM_READGROUP_ID},
280     {"splice-mismatches", required_argument, 0, OPT_SPLICE_MISMATCHES},
281     {"verbose", no_argument, 0, OPT_VERBOSE},
282     {"inner-dist-mean", required_argument, 0, OPT_INSERT_LENGTH_MEAN},
283     {"inner-dist-std-dev", required_argument, 0, OPT_INSERT_LENGTH_STD_DEV},
284     {"output-dir", required_argument, 0, OPT_OUTPUT_DIR},
285     {"gene-filter", required_argument, 0, OPT_GENE_FILTER},
286     {"gtf-annotations", required_argument, 0, OPT_GFF_ANNOTATIONS},
287     {"max-multihits", required_argument, 0, OPT_MAX_MULTIHITS},
288     {"no-closure-search", no_argument, 0, OPT_NO_CLOSURE_SEARCH},
289     {"no-coverage-search", no_argument, 0, OPT_NO_COVERAGE_SEARCH},
290     {"no-microexon-search", no_argument, 0, OPT_NO_MICROEXON_SEARCH},
291     {"segment-length", required_argument, 0, OPT_SEGMENT_LENGTH},
292     {"segment-mismatches", required_argument, 0, OPT_SEGMENT_MISMATCHES},
293     {"min-closure-exon", required_argument, 0, OPT_MIN_CLOSURE_EXON},
294     {"min-closure-intron", required_argument, 0, OPT_MIN_CLOSURE_INTRON},
295     {"max-closure-intron", required_argument, 0, OPT_MAX_CLOSURE_INTRON},
296     {"min-coverage-intron", required_argument, 0, OPT_MIN_COVERAGE_INTRON},
297     {"max-coverage-intron", required_argument, 0, OPT_MAX_COVERAGE_INTRON},
298     {"min-segment-intron", required_argument, 0, OPT_MIN_SEGMENT_INTRON},
299     {"max-segment-intron", required_argument, 0, OPT_MAX_SEGMENT_INTRON},
300     {"min-report-intron", required_argument, 0, OPT_MIN_REPORT_INTRON},
301     {"max-report-intron", required_argument, 0, OPT_MAX_REPORT_INTRON},
302     {"min-isoform-fraction",required_argument, 0, OPT_MIN_ISOFORM_FRACTION},
303     {"ium-reads", required_argument, 0, OPT_IUM_READS},
304     {"butterfly-search", no_argument, 0, OPT_BUTTERFLY_SEARCH},
305     {"solexa-quals", no_argument, 0, OPT_SOLEXA_QUALS},
306     {"phred64-quals", no_argument, 0, OPT_PHRED64_QUALS},
307     {"quals", no_argument, 0, OPT_QUALS},
308     {"integer-quals", no_argument, 0, OPT_INTEGER_QUALS},
309     {"color", no_argument, 0, OPT_COLOR},
310     {"color-out", no_argument, 0, OPT_COLOR_OUT},
311     {"library-type", required_argument, 0, OPT_LIBRARY_TYPE},
312     {"max-deletion-length", required_argument, 0, OPT_MAX_DELETION_LENGTH},
313     {"max-insertion-length", required_argument, 0, OPT_MAX_INSERTION_LENGTH},
314     {"num-threads", required_argument, 0, OPT_NUM_CPUS},
315     {"zpacker", required_argument, 0, OPT_ZPACKER},
316     {"samtools", required_argument, 0, OPT_SAMTOOLS},
317     {"aux-outfile", required_argument, 0, OPT_AUX_OUT},
318     {"gtf-juncs", required_argument, 0, OPT_GTF_JUNCS},
319     {0, 0, 0, 0} // terminator
320     };
321    
322    
323     void str_appendInt(string& str, int v) {
324     stringstream ss;
325     ss << v;
326     str.append(ss.str());
327     }
328    
329     bool str_endsWith(string& str, const char* suffix) {
330     if (str.empty() || str.length()<3) return false;
331     size_t l=strlen(suffix);
332     if (str.length()<=l) return false;
333     if (str.rfind(suffix, str.length()-l-1)!=string::npos) return true;
334     return false;
335     }
336    
337     int parse_options(int argc, char** argv, void (*print_usage)())
338     {
339     int option_index = 0;
340     int next_option;
341     do {
342     next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
343     switch (next_option) {
344     case -1:
345     break;
346     case OPT_FASTA:
347     reads_format = FASTA;
348     break;
349     case OPT_FASTQ:
350     reads_format = FASTQ;
351     break;
352     case OPT_MIN_ANCHOR:
353     min_anchor_len = (uint32_t)parseIntOpt(3, "--min-anchor arg must be at least 3", print_usage);
354     break;
355     case OPT_SPLICE_MISMATCHES:
356     max_splice_mismatches = parseIntOpt(0, "--splice-mismatches arg must be at least 0", print_usage);
357     break;
358     case OPT_VERBOSE:
359     verbose = true;
360     break;
361     case OPT_INSERT_LENGTH_MEAN:
362     inner_dist_mean = parseIntOpt(-1024, "--inner-dist-mean arg must be at least -1024", print_usage);
363     break;
364     case OPT_INSERT_LENGTH_STD_DEV:
365     inner_dist_std_dev = parseIntOpt(0, "--inner-dist-std-dev arg must be at least 0", print_usage);
366     break;
367     case OPT_OUTPUT_DIR:
368     output_dir = optarg;
369     break;
370     case OPT_GENE_FILTER:
371     gene_filter = optarg;
372     break;
373     case OPT_GFF_ANNOTATIONS:
374     gff_file = optarg;
375     break;
376     case OPT_MAX_MULTIHITS:
377     max_multihits = parseIntOpt(1, "--max-multihits arg must be at least 1", print_usage);
378     break;
379     case OPT_NO_CLOSURE_SEARCH:
380     no_closure_search = true;
381     break;
382     case OPT_NO_COVERAGE_SEARCH:
383     no_coverage_search = true;
384     break;
385     case OPT_NO_MICROEXON_SEARCH:
386     no_microexon_search = true;
387     break;
388     case OPT_SEGMENT_LENGTH:
389     segment_length = parseIntOpt(4, "--segment-length arg must be at least 4", print_usage);
390     break;
391     case OPT_SEGMENT_MISMATCHES:
392     segment_mismatches = parseIntOpt(0, "--segment-mismatches arg must be at least 0", print_usage);
393     break;
394     case OPT_MIN_CLOSURE_EXON:
395     min_closure_exon_length = parseIntOpt(1, "--min-closure-exon arg must be at least 1", print_usage);
396     break;
397     case OPT_MIN_CLOSURE_INTRON:
398     min_closure_intron_length = parseIntOpt(1, "--min-closure-intron arg must be at least 1", print_usage);
399     break;
400     case OPT_MAX_CLOSURE_INTRON:
401     max_closure_intron_length = parseIntOpt(1, "--max-closure-intron arg must be at least 1", print_usage);
402     break;
403     case OPT_MIN_COVERAGE_INTRON:
404     min_coverage_intron_length = parseIntOpt(1, "--min-coverage-intron arg must be at least 1", print_usage);
405     break;
406     case OPT_MAX_COVERAGE_INTRON:
407     max_coverage_intron_length = parseIntOpt(1, "--max-coverage-intron arg must be at least 1", print_usage);
408     break;
409     case OPT_MIN_SEGMENT_INTRON:
410     min_segment_intron_length = parseIntOpt(1, "--min-segment-intron arg must be at least 1", print_usage);
411     break;
412     case OPT_MAX_SEGMENT_INTRON:
413     max_segment_intron_length = parseIntOpt(1, "--max-segment-intron arg must be at least 1", print_usage);
414     break;
415     case OPT_MIN_REPORT_INTRON:
416     min_report_intron_length = parseIntOpt(1, "--min-report-intron arg must be at least 1", print_usage);
417     break;
418     case OPT_MAX_REPORT_INTRON:
419     max_report_intron_length = parseIntOpt(1, "--max-report-intron arg must be at least 1", print_usage);
420     break;
421     case OPT_MIN_ISOFORM_FRACTION:
422     min_isoform_fraction = parseFloatOpt(0.0f, 1.0f, "--min-isoform-fraction arg must be [0.0,1.0]", print_usage);
423     break;
424     case OPT_IUM_READS:
425     ium_reads = optarg;
426     break;
427     case OPT_SAM_HEADER:
428     sam_header = optarg;
429     break;
430     case OPT_SAM_READGROUP_ID:
431     sam_readgroup_id = optarg;
432     break;
433     case OPT_BUTTERFLY_SEARCH:
434     butterfly_search = true;
435     break;
436     case OPT_SOLEXA_QUALS:
437     solexa_quals = true;
438     break;
439     case OPT_PHRED64_QUALS:
440     phred64_quals = true;
441     break;
442     case 'Q':
443     case OPT_QUALS:
444     quals = true;
445     break;
446     case OPT_INTEGER_QUALS:
447     integer_quals = true;
448     break;
449     case 'C':
450     case OPT_COLOR:
451     color = true;
452     break;
453     case OPT_COLOR_OUT:
454     color_out = true;
455     break;
456     case OPT_LIBRARY_TYPE:
457     if (strcmp(optarg, "fr-unstranded") == 0)
458     library_type = FR_UNSTRANDED;
459     else if (strcmp(optarg, "fr-firststrand") == 0)
460     library_type = FR_FIRSTSTRAND;
461     else if (strcmp(optarg, "fr-secondstrand") == 0)
462     library_type = FR_SECONDSTRAND;
463     else if (strcmp(optarg, "ff-unstranded") == 0)
464     library_type = FF_UNSTRANDED;
465     else if (strcmp(optarg, "ff-firststrand") == 0)
466     library_type = FF_FIRSTSTRAND;
467     else if (strcmp(optarg, "ff-secondstrand") == 0)
468     library_type = FF_SECONDSTRAND;
469     break;
470     case OPT_MAX_DELETION_LENGTH:
471     max_deletion_length = parseIntOpt(0, "--max-deletion-length must be at least 0", print_usage);
472     break;
473     case OPT_MAX_INSERTION_LENGTH:
474     max_insertion_length = parseIntOpt(0, "--max-insertion-length must be at least 0", print_usage);
475     break;
476     case 'z':
477     case OPT_ZPACKER:
478     zpacker = optarg;
479     break;
480     case OPT_SAMTOOLS:
481     samtools_path = optarg;
482     break;
483     case OPT_AUX_OUT:
484     aux_outfile = optarg;
485     break;
486     case 'p':
487     case OPT_NUM_CPUS:
488     num_cpus=parseIntOpt(1,"-p/--num-threads must be at least 1",print_usage);
489     break;
490     case OPT_GTF_JUNCS:
491     gtf_juncs = optarg;
492     break;
493     default:
494     print_usage();
495     return 1;
496     }
497     } while(next_option != -1);
498    
499     return 0;
500     }
501    
502    
503     // Error routine (prints error message and exits!)
504     void err_exit(const char* format,...){
505     va_list arguments;
506     va_start(arguments,format);
507     vfprintf(stderr,format,arguments);
508     va_end(arguments);
509     #ifdef DEBUG
510     // trigger a core dump for later inspection
511     abort();
512     #endif
513     exit(1);
514     }
515    
516     FILE* FZPipe::openRead(const char* fname, string& popencmd) {
517     pipecmd=popencmd;
518     filename=fname;
519     if (pipecmd.empty()) {
520     file=fopen(filename.c_str(), "r");
521     }
522     else {
523     string pcmd(pipecmd);
524     pcmd.append(" '");
525     pcmd.append(filename);
526     pcmd.append("'");
527     file=popen(pcmd.c_str(), "r");
528     }
529     return file;
530     }
531    
532     FILE* FZPipe::openRead(const char* fname) {
533     string pcmd;
534     return this->openRead(fname,pcmd);
535     }
536    
537     FILE* FZPipe::openWrite(const char* fname, string& popencmd) {
538     pipecmd=popencmd;
539     filename=fname;
540     if (pipecmd.empty()) {
541     file=fopen(filename.c_str(), "w");
542     }
543     else {
544     string pcmd(pipecmd);
545     pcmd.append(" - > '");
546     pcmd.append(filename.c_str());
547     pcmd.append("'");
548     file=popen(pcmd.c_str(), "w");
549     }
550     return file;
551     }
552    
553    
554     FILE* FZPipe::openWrite(const char* fname) {
555     string pcmd;
556     return this->openWrite(fname,pcmd);
557     }
558    
559     void FZPipe::rewind() {
560     if (pipecmd.empty()) {
561     if (file!=NULL) {
562     ::rewind(file);
563     return;
564     }
565     if (!filename.empty()) {
566     file=fopen(filename.c_str(),"r");
567     return;
568     }
569     }
570     if (filename.empty())
571     err_die("Error: FZStream::rewind() failed (missing filename)!\n");
572     this->close();
573     string pcmd(pipecmd);
574     pcmd.append(" '");
575     pcmd.append(filename);
576     pcmd.append("'");
577     file=popen(pcmd.c_str(), "r");
578     if (file==NULL) {
579     err_die("Error: FZStream::rewind() popen(%s) failed!\n",pcmd.c_str());
580     }
581     }
582    
583    
584     string getFext(const string& s) {
585     string r("");
586     //if (xpos!=NULL) *xpos=0;
587     if (s.empty() || s=="-") return r;
588     int slen=(int)s.length();
589     int p=s.rfind('.');
590     int d=s.rfind('/');
591     if (p<=0 || p>slen-2 || p<slen-7 || p<d) return r;
592     r=s.substr(p+1);
593     //if (xpos!=NULL) *xpos=p+1;
594     for(size_t i=0; i!=r.length(); i++)
595     r[i] = std::tolower(r[i]);
596     return r;
597     }
598    
599     string guess_packer(const string& fname, bool use_all_cpus) {
600     //only needed for the primary input files (given by user)
601     string picmd("");
602     string fext=getFext(fname);
603 gpertea 32 if (fext=="bam") {
604     picmd="bam2fastx";
605     return picmd;
606     }
607 gpertea 29 if (fext=="gz" || fext=="gzip" || fext=="z") {
608     if (use_all_cpus && str_endsWith(zpacker,"pigz")) {
609     picmd=zpacker;
610     if (num_cpus<2) picmd.append(" -p1");
611     else {
612     picmd.append(" -p");
613     str_appendInt(picmd, num_cpus);
614     //picmd.append(" -cd");
615     }
616     }
617     else picmd="gzip";
618     }
619     else if (fext=="bz2" || fext=="bzip2" || fext=="bz" || fext=="bzip") {
620     if (use_all_cpus && str_endsWith(zpacker,"pbzip2")) {
621     picmd=zpacker;
622     if (num_cpus<2) picmd.append(" -p1");
623     else {
624     picmd.append(" -p");
625     str_appendInt(picmd, num_cpus);
626     //picmd.append(" -cd");
627     }
628     }
629     else picmd="bzip2";
630     }
631     return picmd;
632     }
633    
634     /*
635     string getBam2SamCmd(const string& fname) {
636     string pipecmd("");
637     string fext=getFext(fname);
638     if (fext=="bam") {
639     pipecmd=samtools_path;
640     pipecmd.append(" view");
641     }
642     return pipecmd;
643     }
644     */
645    
646     void err_die(const char* format,...) { // Error exit
647     va_list arguments;
648     va_start(arguments,format);
649     vfprintf(stderr,format,arguments);
650     va_end(arguments);
651     exit(1);
652     }
653    
654     string getUnpackCmd(const string& fname, bool use_all_cpus) {
655 gpertea 32 //prep_reads should use guess_packer() instead
656 gpertea 29 string pipecmd("");
657 gpertea 32 string fext=getFext(fname);
658     if (fext=="bam") {
659     pipecmd="bam2fastx";
660     return pipecmd;
661     }
662     if (zpacker.empty() || fext!="z") {
663 gpertea 29 return pipecmd;
664     }
665     pipecmd=zpacker;
666     if (str_endsWith(pipecmd, "pigz") ||str_endsWith(pipecmd, "pbzip2")) {
667     if (use_all_cpus==false) pipecmd.append(" -p1");
668     else if (num_cpus>1) {
669     pipecmd.append(" -p");
670     str_appendInt(pipecmd,num_cpus);
671     }
672     }
673     if (!pipecmd.empty()) pipecmd.append(" -cd");
674     return pipecmd;
675     }
676    
677     void checkSamHeader() {
678     if (sam_header.empty())
679     err_die("Error: writeSamHeader() with empty sam_header string\n");
680     //copy the SAM header
681     FILE* fh=fopen(sam_header.c_str(), "r");
682     if (fh==NULL)
683     err_die("Error: cannot open SAM header file %s\n",sam_header.c_str());
684     fclose(fh);
685     }
686    
687     void writeSamHeader(FILE* fout) {
688     if (fout==NULL)
689     err_die("Error: writeSamHeader(NULL)\n");
690     checkSamHeader();
691     //copy the SAM header
692     FILE* fh=fopen(sam_header.c_str(), "r");
693     int ch=-1;
694     while ((ch=fgetc(fh))!=EOF) {
695     if (fputc(ch, fout)==EOF)
696     err_die("Error copying SAM header\n");
697     }
698     fclose(fh);
699     }
700    
701     //auxiliary functions for BAM record handling
702     uint8_t* realloc_bdata(bam1_t *b, int size) {
703     if (b->m_data < size) {
704     b->m_data = size;
705     kroundup32(b->m_data);
706     b->data = (uint8_t*)realloc(b->data, b->m_data);
707     }
708     if (b->data_len<size) b->data_len=size;
709     return b->data;
710     }
711    
712     uint8_t* dupalloc_bdata(bam1_t *b, int size) {
713     //same as realloc_bdata, but does not free previous data
714     //but returns it instead
715     //it ALWAYS duplicates data
716     b->m_data = size;
717     kroundup32(b->m_data);
718     uint8_t* odata=b->data;
719     b->data = (uint8_t*)malloc(b->m_data);
720     memcpy((void*)b->data, (void*)odata, b->data_len);
721     b->data_len=size;
722     return odata; //user must FREE this after
723     }
724    
725     extern unsigned short bam_char2flag_table[];
726    
727     GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid,
728     int pos, bool reverse, const char* qseq, const char* cigar, const char* quals) {
729     novel=true;
730     b=bam_init1();
731     b->core.tid=gseq_tid;
732     if (pos<=0) {
733     b->core.pos=-1; //unmapped
734     //if (gseq_tid<0)
735     b->core.flag |= BAM_FUNMAP;
736     }
737     else b->core.pos=pos-1; //BAM is 0-based
738     b->core.qual=255;
739     int l_qseq=strlen(qseq);
740     //this may not be accurate, setting CIGAR is the correct way
741     //b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1);
742     b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
743     memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
744     set_cigar(cigar); //this will also set core.bin
745     add_sequence(qseq, l_qseq);
746     add_quals(quals); //quals must be given as Phred33
747     if (reverse) { b->core.flag |= BAM_FREVERSE ; }
748     }
749    
750     GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
751     int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
752     int insert_size, const char* qseq, const char* quals,
753     const vector<string>* aux_strings) {
754     novel=true;
755     b=bam_init1();
756     b->core.tid=g_tid;
757     b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based
758     b->core.qual=map_qual;
759     int l_qseq=strlen(qseq);
760     b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
761     memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
762     set_cigar(cigar); //this will also set core.bin
763     add_sequence(qseq, l_qseq);
764     add_quals(quals); //quals must be given as Phred33
765     set_flags(flags);
766     set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size);
767     if (aux_strings!=NULL) {
768     for (vector<string>::const_iterator itr=aux_strings->begin();
769     itr!=aux_strings->end(); ++itr) {
770     add_aux(itr->c_str());
771     }
772     }
773     }
774     void GBamRecord::set_cigar(const char* cigar) {
775     //requires b->core.pos and b->core.flag to have been set properly PRIOR to this call
776     int doff=b->core.l_qname;
777     uint8_t* after_cigar=NULL;
778     int after_cigar_len=0;
779     uint8_t* prev_bdata=NULL;
780     if (b->data_len>doff) {
781     //cigar string already allocated, replace it
782     int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data
783     after_cigar=b->data+d;
784     after_cigar_len=b->data_len-d;
785     }
786     const char *s;
787     char *t;
788     int i, op;
789     long x;
790     b->core.n_cigar = 0;
791     if (cigar != NULL && strcmp(cigar, "*") != 0) {
792     for (s = cigar; *s; ++s) {
793     if (isalpha(*s)) b->core.n_cigar++;
794     else if (!isdigit(*s)) {
795     err_die("Error: invalid CIGAR character (%s)\n",cigar);
796     }
797     }
798     if (after_cigar_len>0) { //replace/insert into existing full data
799     prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len);
800     memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len);
801     free(prev_bdata);
802     }
803     else {
804     realloc_bdata(b, doff + b->core.n_cigar * 4);
805     }
806     for (i = 0, s = cigar; i != b->core.n_cigar; ++i) {
807     x = strtol(s, &t, 10);
808     op = toupper(*t);
809     if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
810     else if (op == 'I') op = BAM_CINS;
811     else if (op == 'D') op = BAM_CDEL;
812     else if (op == 'N') op = BAM_CREF_SKIP;
813     else if (op == 'S') op = BAM_CSOFT_CLIP;
814     else if (op == 'H') op = BAM_CHARD_CLIP;
815     else if (op == 'P') op = BAM_CPAD;
816     else err_die("Error: invalid CIGAR operation (%s)\n",cigar);
817     s = t + 1;
818     bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
819     }
820     if (*s) err_die("Error: unmatched CIGAR operation (%s)\n",cigar);
821     b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
822     } else {//no CIGAR string given
823     if (!(b->core.flag&BAM_FUNMAP)) {
824     fprintf(stderr, "Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data);
825     b->core.flag |= BAM_FUNMAP;
826     }
827     b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1);
828     }
829     } //set_cigar()
830    
831     void GBamRecord::add_sequence(const char* qseq, int slen) {
832     //must be called AFTER set_cigar (cannot replace existing sequence for now)
833     if (qseq==NULL) return; //should we ever care about this?
834     if (slen<0) slen=strlen(qseq);
835     int doff = b->core.l_qname + b->core.n_cigar * 4;
836     if (strcmp(qseq, "*")!=0) {
837     b->core.l_qseq=slen;
838     if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b)))
839     err_die("Error: CIGAR and sequence length are inconsistent!(%s)\n",
840     qseq);
841     uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff;
842     //also allocated quals memory
843     memset(p, 0, (b->core.l_qseq+1)/2);
844     for (int i = 0; i < b->core.l_qseq; ++i)
845     p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2);
846     } else b->core.l_qseq = 0;
847     }
848    
849     void GBamRecord::add_quals(const char* quals) {
850     //requires core.l_qseq already set
851     //and must be called AFTER add_sequence(), which also allocates the memory for quals
852     uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2);
853     if (quals==NULL || strcmp(quals, "*") == 0) {
854     for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff;
855     return;
856     }
857     for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33;
858     }
859    
860     void GBamRecord::add_aux(const char* str) {
861     //requires: being called AFTER add_quals()
862     static char tag[2];
863     static uint8_t abuf[512];
864     //requires: being called AFTER add_quals()
865     int strl=strlen(str);
866     //int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux;
867     //int doff0=doff;
868     if (strl < 6 || str[2] != ':' || str[4] != ':')
869     parse_error("missing colon in auxiliary data");
870     tag[0] = str[0]; tag[1] = str[1];
871     uint8_t atype = str[3];
872     uint8_t* adata=abuf;
873     int alen=0;
874     if (atype == 'A' || atype == 'a' || atype == 'c' || atype == 'C') { // c and C for backward compatibility
875     atype='A';
876     alen=1;
877     adata=(uint8_t*)&str[5];
878     }
879     else if (atype == 'I' || atype == 'i') {
880     long long x=(long long)atoll(str + 5);
881     if (x < 0) {
882     if (x >= -127) {
883     atype='c';
884     abuf[0] = (int8_t)x;
885     alen=1;
886     }
887     else if (x >= -32767) {
888     atype = 's';
889     *(int16_t*)abuf = (int16_t)x;
890     alen=2;
891     }
892     else {
893     atype='i';
894     *(int32_t*)abuf = (int32_t)x;
895     alen=4;
896     if (x < -2147483648ll)
897     fprintf(stderr, "Parse warning: integer %lld is out of range.",
898     x);
899     }
900     } else { //x >=0
901     if (x <= 255) {
902     atype = 'C';
903     abuf[0] = (uint8_t)x;
904     alen=1;
905     }
906     else if (x <= 65535) {
907     atype='S';
908     *(uint16_t*)abuf = (uint16_t)x;
909     alen=2;
910     }
911     else {
912     atype='I';
913     *(uint32_t*)abuf = (uint32_t)x;
914     alen=4;
915     if (x > 4294967295ll)
916     fprintf(stderr, "Parse warning: integer %lld is out of range.",
917     x);
918     }
919     }
920     } //integer type
921     else if (atype == 'f') {
922     *(float*)abuf = (float)atof(str + 5);
923     alen = sizeof(float);
924     }
925     else if (atype == 'd') { //?
926     *(float*)abuf = (float)atof(str + 9);
927     alen=8;
928     }
929     else if (atype == 'Z' || atype == 'H') {
930     if (atype == 'H') { // check whether the hex string is valid
931     if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even");
932     for (int i = 0; i < strl - 5; ++i) {
933     int c = toupper(str[5 + i]);
934     if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
935     parse_error("invalid hex character");
936     }
937     }
938     memcpy(abuf, str + 5, strl - 5);
939     abuf[strl-5] = 0;
940     alen=strl-4;
941     } else parse_error("unrecognized aux type");
942     this->add_aux(tag, atype, alen, adata);
943     }//add_aux()