nvbio::alndiff Namespace Reference

Classes
struct	Alignment
struct	AlignmentPair
struct	AlignmentStream
struct	BAMAlignmentStream
struct	DebugAlignmentStream
struct	Filter
struct	PEAnalyzer
struct	SEAnalyzer
struct	StatsPartition
struct	Stats
struct	AlignmentStats
struct	BooleanStats
struct	Histogram
struct	Histogram2d

Enumerations
enum	Type { LOWER = 0, HIGHER = 1 }
enum	Bins { LINEAR = 0, LOG = 1 }

Functions
AlignmentStream *	open_dbg_file (const char *file_name)
AlignmentStream *	open_bam_file (const char *file_name)
AlignmentStream *	open_alignment_file (const char *file_name)
bool	distant (const Alignment &a1, const Alignment &a2)
std::string	generate_file_name (const char *report, const char *name)
void	add_param (FILE *html_output, const char *name, const uint32 val, bool alt)
void	add_param (FILE *html_output, const char *name, const float val, bool alt)
void	add_param (FILE *html_output, const char *name, const char *val, bool alt)
template<typename T >
void	find_gt2 (const int32 first_row, const int32 last_row, const T &table, int32 best_bin[2])
template<uint32 XX>
int32	first_display_row (const Histogram< XX > &table, const uint32 total, const int32 last_row=0)
template<uint32 XX>
int32	last_display_row (const Histogram< XX > &table, const uint32 total, const int32 first_row=0)
template<uint32 XX>
int2	display_range (const Histogram< XX > &table, const uint32 total)
void	stats_string (char *buffer, const float v, const float range)
template<uint32 XX>
void	generate_diff_table (FILE *html_output, const char *stat_by, const char *name, const Bins bin_type, const Histogram< XX > &stats_l, const Histogram< XX > &stats_r, const uint32 total, const uint32 n_mapped_both)
template<uint32 XX>
void	generate_table (FILE *html_output, const char *stat_by, const char *name, const Bins bin_type, const Histogram< XX > &stats, const uint32 total)
template<uint32 XX>
void	generate_table (FILE *html_output, const char *stat_by, const char *name, const Bins bin_type, const Histogram< XX > &stats_l, const Histogram< XX > &stats_r, const uint32 l_count, const uint32 r_count)
template<uint32 XX, uint32 YY>
void	generate_table2d (FILE *html_output, const char *stat_by, const char *name, const Histogram2d< XX, YY > &stats_l, const Histogram2d< XX, YY > &stats_r, const char *bin_name, const std::vector< std::string > &X_bins, const std::vector< std::string > &Y_bins, const uint32 total, const uint32 n_mapped_both, const bool diff_table)
void	generate_table (const char *file_name, const char *stat_by, const char *name, const char *diff_name, const Bins bin_type, const StatsPartition &stats_l, const StatsPartition &stats_r, const uint32 total, const uint32 n_mapped_both, const bool absolute_values=true)
template<uint32 X>
Histogram< X >	cumulative (const Histogram< X > &I)
template<uint32 X>
Histogram< X >	reverse_cumulative (const Histogram< X > &I)
uint32	read_length_bin_range (const uint32 bin)
uint32	read_length_bin (const uint32 read_len)
int32	log_bin (const int32 x)
int32	log_bin_range (const int32 bin)
const char *	local_file (const std::string &file_name)

Enumeration Type Documentation

enum nvbio::alndiff::Bins

Enumerator
LINEAR
LOG

Definition at line 37 of file stats.h.

enum nvbio::alndiff::Type

Enumerator
LOWER
HIGHER

Definition at line 36 of file stats.h.

Function Documentation

void nvbio::alndiff::add_param ( FILE *  html_output, const char *  name, const uint32  val, bool  alt  )

inline

Definition at line 51 of file html.h.

void nvbio::alndiff::add_param ( FILE *  html_output, const char *  name, const float  val, bool  alt  )

inline

Definition at line 58 of file html.h.

void nvbio::alndiff::add_param ( FILE *  html_output, const char *  name, const char *  val, bool  alt  )

inline

Definition at line 65 of file html.h.

template<uint32 X>

Histogram<X> nvbio::alndiff::cumulative

(

const Histogram< X > &

I)

Definition at line 92 of file utils.h.

template<uint32 XX>

int2 nvbio::alndiff::display_range	(	const Histogram< XX > &	table,
		const uint32	total
	)

Definition at line 132 of file html.h.

bool nvbio::alndiff::distant ( const Alignment &  a1, const Alignment &  a2  )

inline

Definition at line 99 of file alignment.h.

template<typename T >

void nvbio::alndiff::find_gt2	(	const int32	first_row,
		const int32	last_row,
		const T &	table,
		int32	best_bin[2]
	)

Definition at line 75 of file html.h.

template<uint32 XX>

int32 nvbio::alndiff::first_display_row	(	const Histogram< XX > &	table,
		const uint32	total,
		const int32	last_row = 0
	)

Definition at line 100 of file html.h.

template<uint32 XX>

void nvbio::alndiff::generate_diff_table	(	FILE *	html_output,
		const char *	stat_by,
		const char *	name,
		const Bins	bin_type,
		const Histogram< XX > &	stats_l,
		const Histogram< XX > &	stats_r,
		const uint32	total,
		const uint32	n_mapped_both
	)

Definition at line 146 of file html.h.

std::string nvbio::alndiff::generate_file_name ( const char *  report, const char *  name  )

inline

Definition at line 40 of file html.h.

template<uint32 XX>

void nvbio::alndiff::generate_table	(	FILE *	html_output,
		const char *	stat_by,
		const char *	name,
		const Bins	bin_type,
		const Histogram< XX > &	stats,
		const uint32	total
	)

Definition at line 283 of file html.h.

template<uint32 XX>

void nvbio::alndiff::generate_table	(	FILE *	html_output,
		const char *	stat_by,
		const char *	name,
		const Bins	bin_type,
		const Histogram< XX > &	stats_l,
		const Histogram< XX > &	stats_r,
		const uint32	l_count,
		const uint32	r_count
	)

Definition at line 340 of file html.h.

void nvbio::alndiff::generate_table ( const char *  file_name, const char *  stat_by, const char *  name, const char *  diff_name, const Bins  bin_type, const StatsPartition &  stats_l, const StatsPartition &  stats_r, const uint32  total, const uint32  n_mapped_both, const bool  absolute_values = true  )

inline

Definition at line 594 of file html.h.

template<uint32 XX, uint32 YY>

void nvbio::alndiff::generate_table2d	(	FILE *	html_output,
		const char *	stat_by,
		const char *	name,
		const Histogram2d< XX, YY > &	stats_l,
		const Histogram2d< XX, YY > &	stats_r,
		const char *	bin_name,
		const std::vector< std::string > &	X_bins,
		const std::vector< std::string > &	Y_bins,
		const uint32	total,
		const uint32	n_mapped_both,
		const bool	diff_table
	)

Definition at line 405 of file html.h.

template<uint32 XX>

int32 nvbio::alndiff::last_display_row	(	const Histogram< XX > &	table,
		const uint32	total,
		const int32	first_row = 0
	)

Definition at line 116 of file html.h.

const char* nvbio::alndiff::local_file ( const std::string &  file_name)

inline

Definition at line 211 of file utils.h.

int32 nvbio::alndiff::log_bin ( const int32  x)

inline

Definition at line 196 of file utils.h.

int32 nvbio::alndiff::log_bin_range ( const int32  bin)

inline

Definition at line 202 of file utils.h.

AlignmentStream * nvbio::alndiff::open_alignment_file

(

const char *

file_name)

open an alignment file

Definition at line 38 of file alignment.cpp.

AlignmentStream * nvbio::alndiff::open_bam_file

(

const char *

file_name)

Definition at line 147 of file alignment_bam.cpp.

AlignmentStream * nvbio::alndiff::open_dbg_file

(

const char *

file_name)

Definition at line 124 of file alignment_dbg.cpp.

uint32 nvbio::alndiff::read_length_bin ( const uint32  read_len)

inline

Definition at line 169 of file utils.h.

uint32 nvbio::alndiff::read_length_bin_range ( const uint32  bin)

inline

Definition at line 137 of file utils.h.

template<uint32 X>

Histogram<X> nvbio::alndiff::reverse_cumulative

(

const Histogram< X > &

I)

Definition at line 103 of file utils.h.

void nvbio::alndiff::stats_string ( char *  buffer, const float  v, const float  range  )

inline

Definition at line 140 of file html.h.