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root/gclib/tophat_cpp/common.h
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# Line 28 | Line 28
28  
29   extern bool bowtie2;
30   extern int bowtie2_min_score;
31 + extern int bowtie2_max_penalty;
32 + extern int bowtie2_min_penalty;
33 + extern int bowtie2_penalty_for_N;
34 + extern int bowtie2_read_gap_open;
35 + extern int bowtie2_read_gap_cont;
36 + extern int bowtie2_ref_gap_open;
37 + extern int bowtie2_ref_gap_cont;
38  
39   // daehwan - temporary for parallelization
40   extern bool parallel;
# Line 77 | Line 84
84  
85   extern bool verbose;
86   extern unsigned int max_multihits;
87 + extern unsigned int max_seg_multihits;
88   extern bool no_closure_search;
89   extern bool no_coverage_search;
90   extern bool no_microexon_search;
# Line 100 | Line 108
108   extern bool quals;
109   extern bool integer_quals;
110   extern bool color;
103 extern bool color_out;
111   extern std::string gtf_juncs;
112  
113 + extern bool report_secondary_alignments;
114 +
115   //prep_reads only: --flt-reads <bowtie-fastq_for--max>
116   //  filter out reads if their numeric ID is in this fastq file
117   // OR if flt_mappings was given too, filter out reads if their ID
# Line 398 | Line 407
407           err_die("Error: missing SAM header (get_tid())\n");
408        return bam_get_tid(bam_header, seq_name);
409        }
410 +
411     //just a convenience function for creating a new record, but it's NOT written
412     //given pos must be 1-based (so it'll be stored as pos-1 because BAM is 0-based)
413     GBamRecord* new_record(const char* qname, const char* gseqname,
# Line 455 | Line 465
465                   if (idxcount >= 1000 && read_id != idx_last_id) {
466                           int64_t offset = this->tell();
467                           int block_offset = offset & 0xFFFF;
468 +                         //int64_t block_address = (offset >> 16) & 0xFFFFFFFFFFFFLL;
469                           // daehwan - this is a bug in bgzf.c in samtools
470                           // I'll report this bug with a temporary solution, soon.
471 +
472                           if (block_offset <= 0xF000) {
473                             fprintf(findex, "%lu\t%ld\n", read_id, offset);
474                             idxcount = 0;
# Line 473 | Line 485
485       return bam_tell(this->bam_file->x.bam);
486     }
487  
488 <   void updateIndex(uint64_t read_id) {
477 <   }
478 <
488 >  
489     int64_t writtenCount() { return wcount; }
490  
491     void flush() {

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