35 #ifndef MULTOVL_PROB_PIPELINE_HEADER
36 #define MULTOVL_PROB_PIPELINE_HEADER
42 #include "basepipeline.hh"
44 #include "shuffleovl.hh"
45 #include "probopts.hh"
81 typedef std::map<unsigned int, unsigned int>
mtolen_t;
89 void update(
const MultiOverlap::multiregvec_t& overlaps);
152 unsigned int read_tracks(
153 const std::vector<std::string>& inputfiles,
154 unsigned int& trackid,
156 unsigned int read_free_regions(
const std::string& freefile);
157 void write_comments()
const;
164 #endif // MULTOVL_PROB_PIPELINE_HEADER
virtual ProbOpts * opt_ptr()
Definition: probpipeline.hh:132
std::map< std::string, ShuffleOvl > chrom_shufovl_map
There is one ShuffleOvl object for each chromosome.
Definition: probpipeline.hh:101
virtual unsigned int read_input()
MultovlOptbase * opt_pimpl()
Definition: basepipeline.hh:132
void update(const MultiOverlap::multiregvec_t &overlaps)
virtual bool write_output()
const mtolen_t & mtolen() const
Definition: probpipeline.hh:92
OvlenCounter()
Init to empty.
Definition: probpipeline.hh:84
chrom_shufovl_map & csovl()
Definition: probpipeline.hh:138
virtual Stat & stat()
Definition: probpipeline.hh:145
unsigned int calc_actual_overlaps()
Definition: probpipeline.hh:76
std::map< unsigned int, unsigned int > mtolen_t
multiplicity => total overlap length map
Definition: probpipeline.hh:81
virtual unsigned int detect_overlaps()
Option handling for the file-based multovl tools.
Definition: probopts.hh:57
Definition: probpipeline.hh:57
const chrom_shufovl_map & csovl() const
Definition: probpipeline.hh:135
Definition: basepipeline.hh:69
const Stat & stat() const
Definition: probpipeline.hh:141