From 9b7a67a701e9361b9830c4f5aa13f2dbea3e2437 Mon Sep 17 00:00:00 2001 From: dpryan79 Date: Mon, 8 Jan 2018 13:40:08 +0100 Subject: [PATCH] Update documentation for 0.4.2 --- docs/html/annotated.html | 4 +- docs/html/bigWigIO_8h.html | 4 +- docs/html/bigWigIO_8h_source.html | 8 +- docs/html/bigWig_8h.html | 59 +- docs/html/bigWig_8h_source.html | 609 +++++++++--------- docs/html/bwCommon_8h.html | 4 +- docs/html/bwCommon_8h_source.html | 14 +- docs/html/bwValues_8h.html | 4 +- docs/html/bwValues_8h_source.html | 4 +- docs/html/classes.html | 4 +- docs/html/files.html | 4 +- docs/html/functions.html | 4 +- docs/html/functions_vars.html | 4 +- docs/html/globals.html | 50 +- docs/html/globals_defs.html | 5 +- docs/html/globals_enum.html | 5 +- docs/html/globals_eval.html | 40 +- docs/html/globals_func.html | 5 +- docs/html/globals_type.html | 5 +- docs/html/globals_vars.html | 5 +- docs/html/index.html | 4 +- docs/html/md_README.html | 6 +- docs/html/pages.html | 4 +- docs/html/search/all_0.js | 65 +- docs/html/search/all_1.js | 76 ++- docs/html/search/all_10.js | 8 +- docs/html/search/all_11.js | 8 +- docs/html/search/all_12.js | 4 +- docs/html/search/all_13.js | 3 +- docs/html/search/all_14.js | 2 +- docs/html/search/all_15.html | 26 + docs/html/search/all_15.js | 4 + docs/html/search/all_2.js | 19 +- docs/html/search/all_3.js | 10 +- docs/html/search/all_4.js | 9 +- docs/html/search/all_5.js | 7 +- docs/html/search/all_6.js | 2 +- docs/html/search/all_7.js | 9 +- docs/html/search/all_8.js | 16 +- docs/html/search/all_9.js | 12 +- docs/html/search/all_a.js | 17 +- docs/html/search/all_b.js | 11 +- docs/html/search/all_c.js | 2 +- docs/html/search/all_d.js | 5 +- docs/html/search/all_e.js | 13 +- docs/html/search/all_f.js | 13 +- docs/html/search/enumvalues_0.js | 5 +- docs/html/search/enumvalues_1.html | 26 + docs/html/search/enumvalues_1.js | 5 + docs/html/search/enumvalues_2.html | 26 + docs/html/search/enumvalues_2.js | 5 + docs/html/search/enumvalues_3.html | 26 + docs/html/search/enumvalues_3.js | 6 + docs/html/search/enumvalues_4.html | 26 + docs/html/search/enumvalues_4.js | 5 + docs/html/search/search.js | 12 +- docs/html/structURL__t.html | 4 +- docs/html/structbbOverlappingEntries__t.html | 4 +- docs/html/structbigWigFile__t.html | 4 +- docs/html/structbigWigHdr__t.html | 4 +- docs/html/structbwDataHeader__t.html | 4 +- docs/html/structbwOverlapBlock__t.html | 4 +- docs/html/structbwOverlapIterator__t.html | 4 +- .../html/structbwOverlappingIntervals__t.html | 4 +- docs/html/structbwRTreeNode__t.html | 4 +- docs/html/structbwRTree__t.html | 4 +- docs/html/structbwWriteBuffer__t.html | 4 +- docs/html/structbwZoomHdr__t.html | 4 +- docs/html/structchromList__t.html | 4 +- 69 files changed, 834 insertions(+), 556 deletions(-) create mode 100644 docs/html/search/all_15.html create mode 100644 docs/html/search/all_15.js create mode 100644 docs/html/search/enumvalues_1.html create mode 100644 docs/html/search/enumvalues_1.js create mode 100644 docs/html/search/enumvalues_2.html create mode 100644 docs/html/search/enumvalues_2.js create mode 100644 docs/html/search/enumvalues_3.html create mode 100644 docs/html/search/enumvalues_3.js create mode 100644 docs/html/search/enumvalues_4.html create mode 100644 docs/html/search/enumvalues_4.js diff --git a/docs/html/annotated.html b/docs/html/annotated.html index d0ae27b..e413298 100644 --- a/docs/html/annotated.html +++ b/docs/html/annotated.html @@ -71,7 +71,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -105,7 +105,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bigWigIO_8h.html b/docs/html/bigWigIO_8h.html index e702d44..73fa61d 100644 --- a/docs/html/bigWigIO_8h.html +++ b/docs/html/bigWigIO_8h.html @@ -69,7 +69,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -316,7 +316,7 @@

Variable Documentation

-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bigWigIO_8h_source.html b/docs/html/bigWigIO_8h_source.html index b0b54c4..f3c6c42 100644 --- a/docs/html/bigWigIO_8h_source.html +++ b/docs/html/bigWigIO_8h_source.html @@ -70,7 +70,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -136,17 +136,17 @@
GLOBAL_DEFAULTBUFFERSIZE
size_t GLOBAL_DEFAULTBUFFERSIZE
Definition: io.c:12
URL_t::filePos
size_t filePos
Definition: bigWigIO.h:40
URL_t::bufLen
size_t bufLen
Definition: bigWigIO.h:43
-
urlOpen
URL_t * urlOpen(char *fname, CURLcode(*callBack)(CURL *), const char *mode)
Open a local or remote file.
Definition: io.c:159
+
urlOpen
URL_t * urlOpen(char *fname, CURLcode(*callBack)(CURL *), const char *mode)
Open a local or remote file.
Definition: io.c:161
urlSeek
CURLcode urlSeek(URL_t *URL, size_t pos)
Seeks to a given position in a local or remote file.
Definition: io.c:120
URL_t::fname
char * fname
Definition: bigWigIO.h:46
URL_t::memBuf
void * memBuf
Definition: bigWigIO.h:39
URL_t::curl
CURL * curl
Definition: bigWigIO.h:35
URL_t::isCompressed
int isCompressed
Definition: bigWigIO.h:45
-
urlClose
void urlClose(URL_t *URL)
Close a local/remote file.
Definition: io.c:275
+
urlClose
void urlClose(URL_t *URL)
Close a local/remote file.
Definition: io.c:286
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bigWig_8h.html b/docs/html/bigWig_8h.html index 599180f..7b7b649 100644 --- a/docs/html/bigWig_8h.html +++ b/docs/html/bigWig_8h.html @@ -69,7 +69,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -125,7 +125,7 @@ - + @@ -145,17 +145,18 @@ @@ -350,7 +351,7 @@

Macros

#define LIBBIGWIG_VERSION   0.4.0
#define LIBBIGWIG_VERSION   0.4.2
 
#define LIBBIGWIG_CURL   1
 

Enumerations

enum  bwStatsType {
-  doesNotExist = -1, -mean = 0, -average = 0, -stdev = 1, +  doesNotExist = -1, +mean = 0, +average = 0, +stdev = 1,
-  dev = 1, -max = 2, -min = 3, -cov = 4, +  dev = 1, +max = 2, +min = 3, +cov = 4,
-  coverage = 4 +  coverage = 4, +sum = 5
}
 
- +
#define LIBBIGWIG_VERSION   0.4.0#define LIBBIGWIG_VERSION   0.4.2
@@ -369,6 +370,38 @@

Enumeration Type Documentation

An enum that dictates the type of statistic to fetch for a given interval

+ + + + + + + + + + + +
Enumerator
doesNotExist  +

This does nothing

+
mean  +

The mean value

+
average  +

The mean value

+
stdev  +

The standard deviation of the values

+
dev  +

The standard deviation of the values

+
max  +

The maximum value

+
min  +

The minimum value

+
cov  +

The number of bases covered

+
coverage  +

The number of bases covered

+
sum  +

The sum of per-base values

+
@@ -1666,7 +1699,7 @@

Function Documentation

-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bigWig_8h_source.html b/docs/html/bigWig_8h_source.html index 16ac937..9dbb9d3 100644 --- a/docs/html/bigWig_8h_source.html +++ b/docs/html/bigWig_8h_source.html @@ -70,7 +70,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -93,7 +93,7 @@
7 extern "C" {
8 #endif
9 
-
56 #define LIBBIGWIG_VERSION 0.4.0
+
56 #define LIBBIGWIG_VERSION 0.4.2
57 
61 #ifdef NOCURL
62 #define LIBBIGWIG_CURL 0
@@ -116,316 +116,327 @@
92 #define DEFAULT_BLOCKSIZE 32768
93 
97 enum bwStatsType {
-
98  doesNotExist = -1,
-
99  mean = 0,
-
100  average = 0,
-
101  stdev = 1,
-
102  dev = 1,
-
103  max = 2,
-
104  min = 3,
-
105  cov = 4,
-
106  coverage = 4
-
107 };
-
108 
-
109 //Should hide this from end users
-
115 typedef struct {
-
116  uint32_t *level;
-
117  //There's 4 bytes of padding between these
-
118  uint64_t *dataOffset;
-
119  uint64_t *indexOffset;
-
120  bwRTree_t **idx;
-
121 } bwZoomHdr_t;
-
122 
-
128 typedef struct {
-
129  uint16_t version;
-
130  uint16_t nLevels;
-
131  uint64_t ctOffset;
-
132  uint64_t dataOffset;
-
133  uint64_t indexOffset;
-
134  uint16_t fieldCount;
-
135  uint16_t definedFieldCount;
-
136  uint64_t sqlOffset;
-
137  uint64_t summaryOffset;
-
138  uint32_t bufSize;
-
139  uint64_t extensionOffset;
-
140  bwZoomHdr_t *zoomHdrs;
-
141  //total Summary
-
142  uint64_t nBasesCovered;
-
143  double minVal;
-
144  double maxVal;
-
145  double sumData;
-
146  double sumSquared;
-
147 } bigWigHdr_t;
-
148 
-
149 //Should probably replace this with a hash
-
153 typedef struct {
-
154  int64_t nKeys;
-
155  char **chrom;
-
156  uint32_t *len;
-
157 } chromList_t;
-
158 
-
159 //TODO remove from bigWig.h
-
161 typedef struct bwLL bwLL;
-
162 struct bwLL {
-
163  bwRTreeNode_t *node;
-
164  struct bwLL *next;
-
165 };
-
166 typedef struct bwZoomBuffer_t bwZoomBuffer_t;
-
167 struct bwZoomBuffer_t { //each individual entry takes 32 bytes
-
168  void *p;
-
169  uint32_t l, m;
-
170  struct bwZoomBuffer_t *next;
-
171 };
-
173 
-
178 typedef struct {
-
179  uint64_t nBlocks;
-
180  uint32_t blockSize;
-
181  uint64_t nEntries;
-
182  uint64_t runningWidthSum;
-
183  uint32_t tid;
-
184  uint32_t start;
-
185  uint32_t end;
-
186  uint32_t span;
-
187  uint32_t step;
-
188  uint8_t ltype;
-
189  uint32_t l;
-
190  void *p;
-
191  bwLL *firstIndexNode;
-
192  bwLL *currentIndexNode;
-
193  bwZoomBuffer_t **firstZoomBuffer;
-
194  bwZoomBuffer_t **lastZoomBuffer;
-
195  uint64_t *nNodes;
-
196  uLongf compressPsz;
-
197  void *compressP;
-
198 } bwWriteBuffer_t;
-
199 
-
203 typedef struct {
-
204  URL_t *URL;
-
205  bigWigHdr_t *hdr;
-
206  chromList_t *cl;
-
207  bwRTree_t *idx;
-
208  bwWriteBuffer_t *writeBuffer;
-
209  int isWrite;
-
210  int type;
-
211 } bigWigFile_t;
-
212 
-
216 typedef struct {
-
217  uint32_t l;
-
218  uint32_t m;
-
219  uint32_t *start;
-
220  uint32_t *end;
-
221  float *value;
-
222 } bwOverlappingIntervals_t;
-
223 
-
227 typedef struct {
-
228  uint32_t l;
-
229  uint32_t m;
-
230  uint32_t *start;
-
231  uint32_t *end;
-
232  char **str;
-
233 } bbOverlappingEntries_t;
-
234 
-
239 typedef struct {
-
240  bigWigFile_t *bw;
-
241  uint32_t tid;
-
242  uint32_t start;
-
243  uint32_t end;
-
244  uint64_t offset;
-
245  uint32_t blocksPerIteration;
-
246  int withString;
-
247  void *blocks;
-
248  bwOverlappingIntervals_t *intervals;
-
249  bbOverlappingEntries_t *entries;
-
250  void *data;
-
251 } bwOverlapIterator_t;
-
252 
-
260 int bwInit(size_t bufSize);
-
261 
-
266 void bwCleanup(void);
-
267 
-
275 int bwIsBigWig(char *fname, CURLcode (*callBack)(CURL*));
-
276 
-
284 int bbIsBigBed(char *fname, CURLcode (*callBack)(CURL*));
-
285 
-
294 bigWigFile_t *bwOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode);
-
295 
-
303 bigWigFile_t *bbOpen(char *fname, CURLcode (*callBack)(CURL*));
-
304 
-
313 char *bbGetSQL(bigWigFile_t *fp);
-
314 
-
320 void bwClose(bigWigFile_t *fp);
-
321 
-
322 /*******************************************************************************
-
323 *
-
324 * The following are in bwStats.c
-
325 *
-
326 *******************************************************************************/
-
327 
-
335 uint32_t bwGetTid(bigWigFile_t *fp, char *chrom);
-
336 
-
342 void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o);
-
343 
-
349 void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o);
-
350 
-
363 bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end);
-
364 
-
377 bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString);
-
378 
-
393 bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration);
-
394 
-
411 bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration);
-
412 
-
420 bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter);
-
421 
-
426 void bwIteratorDestroy(bwOverlapIterator_t *iter);
-
427 
-
441 bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA);
-
442 
-
455 double *bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
-
456 
-
469 double *bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
-
470 
-
471 //Writer functions
-
472 
-
480 int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms);
-
481 
-
490 chromList_t *bwCreateChromList(char **chroms, uint32_t *lengths, int64_t n);
-
491 
-
499 int bwWriteHdr(bigWigFile_t *bw);
-
500 
-
517 int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n);
-
518 
-
531 int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n);
-
532 
-
549 int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n);
-
550 
-
562 int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n);
-
563 
-
581 int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n);
-
582 
-
593 int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n);
-
594 
-
595 #ifdef __cplusplus
-
596 }
-
597 #endif
-
bigWigHdr_t::summaryOffset
uint64_t summaryOffset
Definition: bigWig.h:137
-
bbDestroyOverlappingEntries
void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o)
Frees space allocated by bbGetOverlappingEntries
Definition: bwValues.c:328
-
bbOverlappingEntries_t
Holds interval:str associations.
Definition: bigWig.h:227
+
98  doesNotExist = -1,
+
99  mean = 0,
+
100  average = 0,
+
101  stdev = 1,
+
102  dev = 1,
+
103  max = 2,
+
104  min = 3,
+
105  cov = 4,
+
106  coverage = 4,
+
107  sum = 5
+
108 };
+
109 
+
110 //Should hide this from end users
+
116 typedef struct {
+
117  uint32_t *level;
+
118  //There's 4 bytes of padding between these
+
119  uint64_t *dataOffset;
+
120  uint64_t *indexOffset;
+
121  bwRTree_t **idx;
+
122 } bwZoomHdr_t;
+
123 
+
129 typedef struct {
+
130  uint16_t version;
+
131  uint16_t nLevels;
+
132  uint64_t ctOffset;
+
133  uint64_t dataOffset;
+
134  uint64_t indexOffset;
+
135  uint16_t fieldCount;
+
136  uint16_t definedFieldCount;
+
137  uint64_t sqlOffset;
+
138  uint64_t summaryOffset;
+
139  uint32_t bufSize;
+
140  uint64_t extensionOffset;
+
141  bwZoomHdr_t *zoomHdrs;
+
142  //total Summary
+
143  uint64_t nBasesCovered;
+
144  double minVal;
+
145  double maxVal;
+
146  double sumData;
+
147  double sumSquared;
+
148 } bigWigHdr_t;
+
149 
+
150 //Should probably replace this with a hash
+
154 typedef struct {
+
155  int64_t nKeys;
+
156  char **chrom;
+
157  uint32_t *len;
+
158 } chromList_t;
+
159 
+
160 //TODO remove from bigWig.h
+
162 typedef struct bwLL bwLL;
+
163 struct bwLL {
+
164  bwRTreeNode_t *node;
+
165  struct bwLL *next;
+
166 };
+
167 typedef struct bwZoomBuffer_t bwZoomBuffer_t;
+
168 struct bwZoomBuffer_t { //each individual entry takes 32 bytes
+
169  void *p;
+
170  uint32_t l, m;
+
171  struct bwZoomBuffer_t *next;
+
172 };
+
174 
+
179 typedef struct {
+
180  uint64_t nBlocks;
+
181  uint32_t blockSize;
+
182  uint64_t nEntries;
+
183  uint64_t runningWidthSum;
+
184  uint32_t tid;
+
185  uint32_t start;
+
186  uint32_t end;
+
187  uint32_t span;
+
188  uint32_t step;
+
189  uint8_t ltype;
+
190  uint32_t l;
+
191  void *p;
+
192  bwLL *firstIndexNode;
+
193  bwLL *currentIndexNode;
+
194  bwZoomBuffer_t **firstZoomBuffer;
+
195  bwZoomBuffer_t **lastZoomBuffer;
+
196  uint64_t *nNodes;
+
197  uLongf compressPsz;
+
198  void *compressP;
+
199 } bwWriteBuffer_t;
+
200 
+
204 typedef struct {
+
205  URL_t *URL;
+
206  bigWigHdr_t *hdr;
+
207  chromList_t *cl;
+
208  bwRTree_t *idx;
+
209  bwWriteBuffer_t *writeBuffer;
+
210  int isWrite;
+
211  int type;
+
212 } bigWigFile_t;
+
213 
+
217 typedef struct {
+
218  uint32_t l;
+
219  uint32_t m;
+
220  uint32_t *start;
+
221  uint32_t *end;
+
222  float *value;
+
223 } bwOverlappingIntervals_t;
+
224 
+
228 typedef struct {
+
229  uint32_t l;
+
230  uint32_t m;
+
231  uint32_t *start;
+
232  uint32_t *end;
+
233  char **str;
+
234 } bbOverlappingEntries_t;
+
235 
+
240 typedef struct {
+
241  bigWigFile_t *bw;
+
242  uint32_t tid;
+
243  uint32_t start;
+
244  uint32_t end;
+
245  uint64_t offset;
+
246  uint32_t blocksPerIteration;
+
247  int withString;
+
248  void *blocks;
+
249  bwOverlappingIntervals_t *intervals;
+
250  bbOverlappingEntries_t *entries;
+
251  void *data;
+
252 } bwOverlapIterator_t;
+
253 
+
261 int bwInit(size_t bufSize);
+
262 
+
267 void bwCleanup(void);
+
268 
+
276 int bwIsBigWig(char *fname, CURLcode (*callBack)(CURL*));
+
277 
+
285 int bbIsBigBed(char *fname, CURLcode (*callBack)(CURL*));
+
286 
+
295 bigWigFile_t *bwOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode);
+
296 
+
304 bigWigFile_t *bbOpen(char *fname, CURLcode (*callBack)(CURL*));
+
305 
+
314 char *bbGetSQL(bigWigFile_t *fp);
+
315 
+
321 void bwClose(bigWigFile_t *fp);
+
322 
+
323 /*******************************************************************************
+
324 *
+
325 * The following are in bwStats.c
+
326 *
+
327 *******************************************************************************/
+
328 
+
336 uint32_t bwGetTid(bigWigFile_t *fp, char *chrom);
+
337 
+
343 void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o);
+
344 
+
350 void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o);
+
351 
+
364 bwOverlappingIntervals_t *bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end);
+
365 
+
378 bbOverlappingEntries_t *bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString);
+
379 
+
394 bwOverlapIterator_t *bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration);
+
395 
+
412 bwOverlapIterator_t *bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration);
+
413 
+
421 bwOverlapIterator_t *bwIteratorNext(bwOverlapIterator_t *iter);
+
422 
+
427 void bwIteratorDestroy(bwOverlapIterator_t *iter);
+
428 
+
442 bwOverlappingIntervals_t *bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA);
+
443 
+
456 double *bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
+
457 
+
470 double *bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type);
+
471 
+
472 //Writer functions
+
473 
+
481 int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms);
+
482 
+
491 chromList_t *bwCreateChromList(char **chroms, uint32_t *lengths, int64_t n);
+
492 
+
500 int bwWriteHdr(bigWigFile_t *bw);
+
501 
+
518 int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n);
+
519 
+
532 int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n);
+
533 
+
550 int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n);
+
551 
+
563 int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n);
+
564 
+
582 int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n);
+
583 
+
594 int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n);
+
595 
+
596 #ifdef __cplusplus
+
597 }
+
598 #endif
+
bigWigHdr_t::summaryOffset
uint64_t summaryOffset
Definition: bigWig.h:138
+
bbDestroyOverlappingEntries
void bbDestroyOverlappingEntries(bbOverlappingEntries_t *o)
Frees space allocated by bbGetOverlappingEntries
Definition: bwValues.c:332
+
bbOverlappingEntries_t
Holds interval:str associations.
Definition: bigWig.h:228
URL_t
This structure holds the file pointers and buffers needed for raw access to local and remote files...
Definition: bigWigIO.h:32
-
bwWriteBuffer_t::nBlocks
uint64_t nBlocks
Definition: bigWig.h:179
-
bigWigHdr_t::zoomHdrs
bwZoomHdr_t * zoomHdrs
Definition: bigWig.h:140
-
bigWigHdr_t::maxVal
double maxVal
Definition: bigWig.h:144
-
bigWigHdr_t::fieldCount
uint16_t fieldCount
Definition: bigWig.h:134
-
bwAppendIntervalSpans
int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n)
Append to a previous block of variable-step entries. If you previously used bwAddIntervalSpans(), this will continue appending more values to the block(s) it created.
Definition: bwWrite.c:468
-
bwAddIntervals
int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Write a new block of bedGraph-like intervals to a bigWig file Adds entries of the form: chromosome st...
Definition: bwWrite.c:347
-
bbGetOverlappingEntries
bbOverlappingEntries_t * bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString)
Return bigBed entries overlapping an interval. Find all bigBed entries overlapping a range and return...
Definition: bwValues.c:570
+
bwWriteBuffer_t::nBlocks
uint64_t nBlocks
Definition: bigWig.h:180
+
bigWigHdr_t::zoomHdrs
bwZoomHdr_t * zoomHdrs
Definition: bigWig.h:141
+
bigWigHdr_t::maxVal
double maxVal
Definition: bigWig.h:145
+
bigWigHdr_t::fieldCount
uint16_t fieldCount
Definition: bigWig.h:135
+
bwAppendIntervalSpans
int bwAppendIntervalSpans(bigWigFile_t *fp, uint32_t *start, float *values, uint32_t n)
Append to a previous block of variable-step entries. If you previously used bwAddIntervalSpans(), this will continue appending more values to the block(s) it created.
Definition: bwWrite.c:495
+
bwAddIntervals
int bwAddIntervals(bigWigFile_t *fp, char **chrom, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Write a new block of bedGraph-like intervals to a bigWig file Adds entries of the form: chromosome st...
Definition: bwWrite.c:374
+
min
Definition: bigWig.h:104
+
bbGetOverlappingEntries
bbOverlappingEntries_t * bbGetOverlappingEntries(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString)
Return bigBed entries overlapping an interval. Find all bigBed entries overlapping a range and return...
Definition: bwValues.c:574
bwCreateHdr
int bwCreateHdr(bigWigFile_t *fp, int32_t maxZooms)
Create a largely empty bigWig header Every bigWig file has a header, this creates the template for on...
Definition: bwWrite.c:56
-
bwWriteBuffer_t::span
uint32_t span
Definition: bigWig.h:186
-
bigWigFile_t::writeBuffer
bwWriteBuffer_t * writeBuffer
Definition: bigWig.h:208
-
bwOverlappingIntervals_t::m
uint32_t m
Definition: bigWig.h:218
-
bwOverlappingIntervals_t::start
uint32_t * start
Definition: bigWig.h:219
-
bwOverlapIterator_t::intervals
bwOverlappingIntervals_t * intervals
Definition: bigWig.h:248
-
bwOverlapIterator_t::offset
uint64_t offset
Definition: bigWig.h:244
-
bbGetSQL
char * bbGetSQL(bigWigFile_t *fp)
Returns a string containing the SQL entry (or NULL). The "auto SQL" field contains the names and va...
Definition: bwRead.c:318
-
bwWriteBuffer_t::start
uint32_t start
Definition: bigWig.h:184
-
bwOverlapIterator_t::entries
bbOverlappingEntries_t * entries
Definition: bigWig.h:249
-
bwOverlapIterator_t::bw
bigWigFile_t * bw
Definition: bigWig.h:240
-
bwOverlappingIntervals_t::l
uint32_t l
Definition: bigWig.h:217
-
bwWriteBuffer_t::l
uint32_t l
Definition: bigWig.h:189
-
chromList_t::len
uint32_t * len
Definition: bigWig.h:156
-
bwWriteBuffer_t::end
uint32_t end
Definition: bigWig.h:185
-
bwOverlapIterator_t::blocksPerIteration
uint32_t blocksPerIteration
Definition: bigWig.h:245
-
bwOpen
bigWigFile_t * bwOpen(char *fname, CURLcode(*callBack)(CURL *), const char *mode)
Opens a local or remote bigWig file. This will open a local or remote bigWig file. Writing of local bigWig files is also supported.
Definition: bwRead.c:348
-
bwWriteBuffer_t::lastZoomBuffer
bwZoomBuffer_t ** lastZoomBuffer
Definition: bigWig.h:194
-
bigWigHdr_t::sumData
double sumData
Definition: bigWig.h:145
+
bwWriteBuffer_t::span
uint32_t span
Definition: bigWig.h:187
+
bigWigFile_t::writeBuffer
bwWriteBuffer_t * writeBuffer
Definition: bigWig.h:209
+
bwOverlappingIntervals_t::m
uint32_t m
Definition: bigWig.h:219
+
bwOverlappingIntervals_t::start
uint32_t * start
Definition: bigWig.h:220
+
doesNotExist
Definition: bigWig.h:98
+
bwOverlapIterator_t::intervals
bwOverlappingIntervals_t * intervals
Definition: bigWig.h:249
+
bwOverlapIterator_t::offset
uint64_t offset
Definition: bigWig.h:245
+
bbGetSQL
char * bbGetSQL(bigWigFile_t *fp)
Returns a string containing the SQL entry (or NULL). The "auto SQL" field contains the names and va...
Definition: bwRead.c:315
+
mean
Definition: bigWig.h:99
+
bwWriteBuffer_t::start
uint32_t start
Definition: bigWig.h:185
+
bwOverlapIterator_t::entries
bbOverlappingEntries_t * entries
Definition: bigWig.h:250
+
bwOverlapIterator_t::bw
bigWigFile_t * bw
Definition: bigWig.h:241
+
bwOverlappingIntervals_t::l
uint32_t l
Definition: bigWig.h:218
+
bwWriteBuffer_t::l
uint32_t l
Definition: bigWig.h:190
+
chromList_t::len
uint32_t * len
Definition: bigWig.h:157
+
bwWriteBuffer_t::end
uint32_t end
Definition: bigWig.h:186
+
bwOverlapIterator_t::blocksPerIteration
uint32_t blocksPerIteration
Definition: bigWig.h:246
+
bwOpen
bigWigFile_t * bwOpen(char *fname, CURLcode(*callBack)(CURL *), const char *mode)
Opens a local or remote bigWig file. This will open a local or remote bigWig file. Writing of local bigWig files is also supported.
Definition: bwRead.c:345
+
bwWriteBuffer_t::lastZoomBuffer
bwZoomBuffer_t ** lastZoomBuffer
Definition: bigWig.h:195
+
bigWigHdr_t::sumData
double sumData
Definition: bigWig.h:146
-
bwWriteBuffer_t::currentIndexNode
bwLL * currentIndexNode
Definition: bigWig.h:192
-
bigWigHdr_t::version
uint16_t version
Definition: bigWig.h:129
-
bigWigFile_t::type
int type
Definition: bigWig.h:210
-
bwWriteBuffer_t::ltype
uint8_t ltype
Definition: bigWig.h:188
-
bwGetTid
uint32_t bwGetTid(bigWigFile_t *fp, char *chrom)
Converts between chromosome name and ID.
Definition: bwValues.c:279
-
bbOverlappingEntries_t::l
uint32_t l
Definition: bigWig.h:228
-
bwOverlapIterator_t
A structure to hold iterations One of intervals and entries should be used to access records from big...
Definition: bigWig.h:239
-
bwWriteBuffer_t::firstZoomBuffer
bwZoomBuffer_t ** firstZoomBuffer
Definition: bigWig.h:193
-
bwWriteHdr
int bwWriteHdr(bigWigFile_t *bw)
Write a the header to a bigWig file. You must have already opened the output file, created a header and a chromosome list.
Definition: bwWrite.c:160
-
bwWriteBuffer_t::nEntries
uint64_t nEntries
Definition: bigWig.h:181
-
bwOverlapIterator_t::tid
uint32_t tid
Definition: bigWig.h:241
-
bbOverlappingEntriesIterator
bwOverlapIterator_t * bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration)
Creates an iterator over entries in a bigBed file Iterators can be traversed with bwIteratorNext() an...
Definition: bwValues.c:610
-
bigWigHdr_t
The header section of a bigWig file.
Definition: bigWig.h:128
-
bigWigHdr_t::sqlOffset
uint64_t sqlOffset
Definition: bigWig.h:136
-
bwGetValues
bwOverlappingIntervals_t * bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA)
Return all per-base bigWig values in a given interval. Given an interval (e.g., chr1:0-100), return the value at each position in a bigWig file. Positions without associated values are suppressed by default, but may be returned if includeNA is not 0.
Definition: bwValues.c:708
-
bwWriteBuffer_t::blockSize
uint32_t blockSize
Definition: bigWig.h:180
-
bwAppendIntervalSpanSteps
int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n)
Append to a previous block of fixed-step entries. If you previously used bwAddIntervalSpanSteps(), this will continue appending more values to the block(s) it created.
Definition: bwWrite.c:525
-
bwAddIntervalSpanSteps
int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n)
Add a new block of fixed-step entries to a bigWig file Adds entries for the form value to the file...
Definition: bwWrite.c:493
-
bwOverlapIterator_t::start
uint32_t start
Definition: bigWig.h:242
-
bigWigHdr_t::bufSize
uint32_t bufSize
Definition: bigWig.h:138
-
bigWigHdr_t::ctOffset
uint64_t ctOffset
Definition: bigWig.h:131
-
bwWriteBuffer_t
This is only needed for writing bigWig files (and won't be created otherwise) This should be removed ...
Definition: bigWig.h:178
-
bwWriteBuffer_t::tid
uint32_t tid
Definition: bigWig.h:183
-
bwZoomHdr_t::idx
bwRTree_t ** idx
Definition: bigWig.h:120
-
bigWigHdr_t::nBasesCovered
uint64_t nBasesCovered
Definition: bigWig.h:142
-
bwIsBigWig
int bwIsBigWig(char *fname, CURLcode(*callBack)(CURL *))
Determine if a file is a bigWig file. This function will quickly check either local or remote files t...
Definition: bwRead.c:305
-
bbOverlappingEntries_t::str
char ** str
Definition: bigWig.h:232
-
bwZoomHdr_t
BigWig files have multiple "zoom" levels, each of which has its own header. This hold those headers...
Definition: bigWig.h:115
-
bbOverlappingEntries_t::start
uint32_t * start
Definition: bigWig.h:230
-
bigWigHdr_t::dataOffset
uint64_t dataOffset
Definition: bigWig.h:132
-
bwOverlapIterator_t::blocks
void * blocks
Definition: bigWig.h:247
-
bwGetOverlappingIntervals
bwOverlappingIntervals_t * bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end)
Return bigWig entries overlapping an interval. Find all bigWig entries overlapping a range and return...
Definition: bwValues.c:558
-
bwWriteBuffer_t::p
void * p
Definition: bigWig.h:190
-
bigWigFile_t::URL
URL_t * URL
Definition: bigWig.h:204
-
bigWigHdr_t::sumSquared
double sumSquared
Definition: bigWig.h:146
+
bwWriteBuffer_t::currentIndexNode
bwLL * currentIndexNode
Definition: bigWig.h:193
+
bigWigHdr_t::version
uint16_t version
Definition: bigWig.h:130
+
bigWigFile_t::type
int type
Definition: bigWig.h:211
+
coverage
Definition: bigWig.h:106
+
bwWriteBuffer_t::ltype
uint8_t ltype
Definition: bigWig.h:189
+
dev
Definition: bigWig.h:102
+
bwGetTid
uint32_t bwGetTid(bigWigFile_t *fp, char *chrom)
Converts between chromosome name and ID.
Definition: bwValues.c:283
+
bbOverlappingEntries_t::l
uint32_t l
Definition: bigWig.h:229
+
bwOverlapIterator_t
A structure to hold iterations One of intervals and entries should be used to access records from big...
Definition: bigWig.h:240
+
bwWriteBuffer_t::firstZoomBuffer
bwZoomBuffer_t ** firstZoomBuffer
Definition: bigWig.h:194
+
bwWriteHdr
int bwWriteHdr(bigWigFile_t *bw)
Write a the header to a bigWig file. You must have already opened the output file, created a header and a chromosome list.
Definition: bwWrite.c:187
+
bwWriteBuffer_t::nEntries
uint64_t nEntries
Definition: bigWig.h:182
+
bwOverlapIterator_t::tid
uint32_t tid
Definition: bigWig.h:242
+
bbOverlappingEntriesIterator
bwOverlapIterator_t * bbOverlappingEntriesIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int withString, uint32_t blocksPerIteration)
Creates an iterator over entries in a bigBed file Iterators can be traversed with bwIteratorNext() an...
Definition: bwValues.c:614
+
bigWigHdr_t
The header section of a bigWig file.
Definition: bigWig.h:129
+
bigWigHdr_t::sqlOffset
uint64_t sqlOffset
Definition: bigWig.h:137
+
bwGetValues
bwOverlappingIntervals_t * bwGetValues(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, int includeNA)
Return all per-base bigWig values in a given interval. Given an interval (e.g., chr1:0-100), return the value at each position in a bigWig file. Positions without associated values are suppressed by default, but may be returned if includeNA is not 0.
Definition: bwValues.c:712
+
average
Definition: bigWig.h:100
+
bwWriteBuffer_t::blockSize
uint32_t blockSize
Definition: bigWig.h:181
+
bwAppendIntervalSpanSteps
int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n)
Append to a previous block of fixed-step entries. If you previously used bwAddIntervalSpanSteps(), this will continue appending more values to the block(s) it created.
Definition: bwWrite.c:552
+
bwAddIntervalSpanSteps
int bwAddIntervalSpanSteps(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t span, uint32_t step, float *values, uint32_t n)
Add a new block of fixed-step entries to a bigWig file Adds entries for the form value to the file...
Definition: bwWrite.c:520
+
bwOverlapIterator_t::start
uint32_t start
Definition: bigWig.h:243
+
bigWigHdr_t::bufSize
uint32_t bufSize
Definition: bigWig.h:139
+
bigWigHdr_t::ctOffset
uint64_t ctOffset
Definition: bigWig.h:132
+
bwWriteBuffer_t
This is only needed for writing bigWig files (and won't be created otherwise) This should be removed ...
Definition: bigWig.h:179
+
bwWriteBuffer_t::tid
uint32_t tid
Definition: bigWig.h:184
+
bwZoomHdr_t::idx
bwRTree_t ** idx
Definition: bigWig.h:121
+
max
Definition: bigWig.h:103
+
bigWigHdr_t::nBasesCovered
uint64_t nBasesCovered
Definition: bigWig.h:143
+
bwIsBigWig
int bwIsBigWig(char *fname, CURLcode(*callBack)(CURL *))
Determine if a file is a bigWig file. This function will quickly check either local or remote files t...
Definition: bwRead.c:302
+
bbOverlappingEntries_t::str
char ** str
Definition: bigWig.h:233
+
bwZoomHdr_t
BigWig files have multiple "zoom" levels, each of which has its own header. This hold those headers...
Definition: bigWig.h:116
+
bbOverlappingEntries_t::start
uint32_t * start
Definition: bigWig.h:231
+
bigWigHdr_t::dataOffset
uint64_t dataOffset
Definition: bigWig.h:133
+
sum
Definition: bigWig.h:107
+
bwOverlapIterator_t::blocks
void * blocks
Definition: bigWig.h:248
+
bwGetOverlappingIntervals
bwOverlappingIntervals_t * bwGetOverlappingIntervals(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end)
Return bigWig entries overlapping an interval. Find all bigWig entries overlapping a range and return...
Definition: bwValues.c:562
+
bwWriteBuffer_t::p
void * p
Definition: bigWig.h:191
+
bigWigFile_t::URL
URL_t * URL
Definition: bigWig.h:205
+
bigWigHdr_t::sumSquared
double sumSquared
Definition: bigWig.h:147
bwCreateChromList
chromList_t * bwCreateChromList(char **chroms, uint32_t *lengths, int64_t n)
Take a list of chromosome names and lengths and return a pointer to a chromList_t This MUST be run be...
Definition: bwWrite.c:22
-
bwAddIntervalSpans
int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n)
Add a new block of variable-step entries to a bigWig file Adds entries for the form chromosome start ...
Definition: bwWrite.c:435
-
bwWriteBuffer_t::step
uint32_t step
Definition: bigWig.h:187
-
bigWigHdr_t::nLevels
uint16_t nLevels
Definition: bigWig.h:130
-
bwWriteBuffer_t::firstIndexNode
bwLL * firstIndexNode
Definition: bigWig.h:191
+
bwAddIntervalSpans
int bwAddIntervalSpans(bigWigFile_t *fp, char *chrom, uint32_t *start, uint32_t span, float *values, uint32_t n)
Add a new block of variable-step entries to a bigWig file Adds entries for the form chromosome start ...
Definition: bwWrite.c:462
+
bwWriteBuffer_t::step
uint32_t step
Definition: bigWig.h:188
+
bigWigHdr_t::nLevels
uint16_t nLevels
Definition: bigWig.h:131
+
bwWriteBuffer_t::firstIndexNode
bwLL * firstIndexNode
Definition: bigWig.h:192
bwInit
int bwInit(size_t bufSize)
Initializes curl and global variables. This MUST be called before other functions (at least if you wa...
Definition: bwRead.c:38
-
bigWigFile_t::hdr
bigWigHdr_t * hdr
Definition: bigWig.h:205
-
bwIteratorDestroy
void bwIteratorDestroy(bwOverlapIterator_t *iter)
Destroys a bwOverlapIterator_t.
Definition: bwValues.c:638
-
bwDestroyOverlappingIntervals
void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o)
Frees space allocated by bwGetOverlappingIntervals
Definition: bwValues.c:320
-
bwOverlapIterator_t::data
void * data
Definition: bigWig.h:250
-
bigWigFile_t::isWrite
int isWrite
Definition: bigWig.h:209
-
bwIteratorNext
bwOverlapIterator_t * bwIteratorNext(bwOverlapIterator_t *iter)
Traverses to the entries/intervals in the next group of blocks.
Definition: bwValues.c:647
-
bwOverlappingIntervals_t::value
float * value
Definition: bigWig.h:221
-
chromList_t::chrom
char ** chrom
Definition: bigWig.h:155
-
bwOverlappingIntervals_t
Holds interval:value associations.
Definition: bigWig.h:216
-
bwWriteBuffer_t::runningWidthSum
uint64_t runningWidthSum
Definition: bigWig.h:182
-
bwStatsFromFull
double * bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:434
-
bigWigHdr_t::definedFieldCount
uint16_t definedFieldCount
Definition: bigWig.h:135
-
bigWigFile_t
A structure that holds everything needed to access a bigWig file.
Definition: bigWig.h:203
-
bwOverlapIterator_t::withString
int withString
Definition: bigWig.h:246
-
bwStats
double * bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:476
+
bigWigFile_t::hdr
bigWigHdr_t * hdr
Definition: bigWig.h:206
+
bwIteratorDestroy
void bwIteratorDestroy(bwOverlapIterator_t *iter)
Destroys a bwOverlapIterator_t.
Definition: bwValues.c:642
+
bwDestroyOverlappingIntervals
void bwDestroyOverlappingIntervals(bwOverlappingIntervals_t *o)
Frees space allocated by bwGetOverlappingIntervals
Definition: bwValues.c:324
+
bwOverlapIterator_t::data
void * data
Definition: bigWig.h:251
+
bigWigFile_t::isWrite
int isWrite
Definition: bigWig.h:210
+
bwIteratorNext
bwOverlapIterator_t * bwIteratorNext(bwOverlapIterator_t *iter)
Traverses to the entries/intervals in the next group of blocks.
Definition: bwValues.c:651
+
bwOverlappingIntervals_t::value
float * value
Definition: bigWig.h:222
+
chromList_t::chrom
char ** chrom
Definition: bigWig.h:156
+
bwOverlappingIntervals_t
Holds interval:value associations.
Definition: bigWig.h:217
+
bwWriteBuffer_t::runningWidthSum
uint64_t runningWidthSum
Definition: bigWig.h:183
+
bwStatsFromFull
double * bwStatsFromFull(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:485
+
bigWigHdr_t::definedFieldCount
uint16_t definedFieldCount
Definition: bigWig.h:136
+
bigWigFile_t
A structure that holds everything needed to access a bigWig file.
Definition: bigWig.h:204
+
bwOverlapIterator_t::withString
int withString
Definition: bigWig.h:247
+
bwStats
double * bwStats(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t nBins, enum bwStatsType type)
Determines per-interval bigWig statistics Can determine mean/min/max/coverage/standard deviation of v...
Definition: bwStats.c:530
bwStatsType
bwStatsType
Definition: bigWig.h:97
-
bigWigFile_t::idx
bwRTree_t * idx
Definition: bigWig.h:207
-
bbIsBigBed
int bbIsBigBed(char *fname, CURLcode(*callBack)(CURL *))
Determine is a file is a bigBed file. This function will quickly check either local or remote files t...
Definition: bwRead.c:335
-
bwWriteBuffer_t::nNodes
uint64_t * nNodes
Definition: bigWig.h:195
-
bbOverlappingEntries_t::m
uint32_t m
Definition: bigWig.h:229
-
bigWigHdr_t::minVal
double minVal
Definition: bigWig.h:143
+
bigWigFile_t::idx
bwRTree_t * idx
Definition: bigWig.h:208
+
bbIsBigBed
int bbIsBigBed(char *fname, CURLcode(*callBack)(CURL *))
Determine is a file is a bigBed file. This function will quickly check either local or remote files t...
Definition: bwRead.c:332
+
bwWriteBuffer_t::nNodes
uint64_t * nNodes
Definition: bigWig.h:196
+
bbOverlappingEntries_t::m
uint32_t m
Definition: bigWig.h:230
+
bigWigHdr_t::minVal
double minVal
Definition: bigWig.h:144
bwCleanup
void bwCleanup(void)
The counterpart to bwInit, this cleans up curl.
Definition: bwRead.c:52
-
bwOverlappingIntervals_t::end
uint32_t * end
Definition: bigWig.h:220
-
chromList_t
Holds the chromosomes and their lengths.
Definition: bigWig.h:153
-
bwOverlapIterator_t::end
uint32_t end
Definition: bigWig.h:243
+
bwOverlappingIntervals_t::end
uint32_t * end
Definition: bigWig.h:221
+
chromList_t
Holds the chromosomes and their lengths.
Definition: bigWig.h:154
+
bwOverlapIterator_t::end
uint32_t end
Definition: bigWig.h:244
bwRTree_t
Definition: bwValues.h:36
-
bwWriteBuffer_t::compressPsz
uLongf compressPsz
Definition: bigWig.h:196
-
bwZoomHdr_t::indexOffset
uint64_t * indexOffset
Definition: bigWig.h:119
-
bigWigHdr_t::indexOffset
uint64_t indexOffset
Definition: bigWig.h:133
-
bwAppendIntervals
int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Append bedGraph-like intervals to a previous block of bedGraph-like intervals in a bigWig file...
Definition: bwWrite.c:407
-
bigWigHdr_t::extensionOffset
uint64_t extensionOffset
Definition: bigWig.h:139
-
bwZoomHdr_t::dataOffset
uint64_t * dataOffset
Definition: bigWig.h:118
-
bigWigFile_t::cl
chromList_t * cl
Definition: bigWig.h:206
-
bwZoomHdr_t::level
uint32_t * level
Definition: bigWig.h:116
+
bwWriteBuffer_t::compressPsz
uLongf compressPsz
Definition: bigWig.h:197
+
bwZoomHdr_t::indexOffset
uint64_t * indexOffset
Definition: bigWig.h:120
+
bigWigHdr_t::indexOffset
uint64_t indexOffset
Definition: bigWig.h:134
+
bwAppendIntervals
int bwAppendIntervals(bigWigFile_t *fp, uint32_t *start, uint32_t *end, float *values, uint32_t n)
Append bedGraph-like intervals to a previous block of bedGraph-like intervals in a bigWig file...
Definition: bwWrite.c:434
+
bigWigHdr_t::extensionOffset
uint64_t extensionOffset
Definition: bigWig.h:140
+
stdev
Definition: bigWig.h:101
+
bwZoomHdr_t::dataOffset
uint64_t * dataOffset
Definition: bigWig.h:119
+
bigWigFile_t::cl
chromList_t * cl
Definition: bigWig.h:207
+
bwZoomHdr_t::level
uint32_t * level
Definition: bigWig.h:117
bwRTreeNode_t
A node within an R-tree holding the index for data.
Definition: bwValues.h:17
-
bbOverlappingEntries_t::end
uint32_t * end
Definition: bigWig.h:231
-
bwClose
void bwClose(bigWigFile_t *fp)
Closes a bigWigFile_t and frees up allocated memory This closes both bigWig and bigBed files...
Definition: bwRead.c:292
-
bwOverlappingIntervalsIterator
bwOverlapIterator_t * bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration)
Creates an iterator over intervals in a bigWig file Iterators can be traversed with bwIteratorNext() ...
Definition: bwValues.c:582
-
chromList_t::nKeys
int64_t nKeys
Definition: bigWig.h:154
-
bwWriteBuffer_t::compressP
void * compressP
Definition: bigWig.h:197
+
bbOverlappingEntries_t::end
uint32_t * end
Definition: bigWig.h:232
+
bwClose
void bwClose(bigWigFile_t *fp)
Closes a bigWigFile_t and frees up allocated memory This closes both bigWig and bigBed files...
Definition: bwRead.c:289
+
bwOverlappingIntervalsIterator
bwOverlapIterator_t * bwOverlappingIntervalsIterator(bigWigFile_t *fp, char *chrom, uint32_t start, uint32_t end, uint32_t blocksPerIteration)
Creates an iterator over intervals in a bigWig file Iterators can be traversed with bwIteratorNext() ...
Definition: bwValues.c:586
+
chromList_t::nKeys
int64_t nKeys
Definition: bigWig.h:155
+
bwWriteBuffer_t::compressP
void * compressP
Definition: bigWig.h:198
-
bbOpen
bigWigFile_t * bbOpen(char *fname, CURLcode(*callBack)(CURL *))
Opens a local or remote bigBed file. This will open a local or remote bigBed file. Note that this file format can only be read and NOT written!
Definition: bwRead.c:387
+
cov
Definition: bigWig.h:105
+
bbOpen
bigWigFile_t * bbOpen(char *fname, CURLcode(*callBack)(CURL *))
Opens a local or remote bigBed file. This will open a local or remote bigBed file. Note that this file format can only be read and NOT written!
Definition: bwRead.c:397
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bwCommon_8h.html b/docs/html/bwCommon_8h.html index 68e04e1..3393186 100644 --- a/docs/html/bwCommon_8h.html +++ b/docs/html/bwCommon_8h.html @@ -69,7 +69,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
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-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bwCommon_8h_source.html b/docs/html/bwCommon_8h_source.html index acb440c..a3b517e 100644 --- a/docs/html/bwCommon_8h_source.html +++ b/docs/html/bwCommon_8h_source.html @@ -70,7 +70,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -101,13 +101,13 @@
61 void destroyBWOverlapBlock(bwOverlapBlock_t *b);
63 
70 int bwFinalize(bigWigFile_t *fp);
-
bwDestroyIndexNode
void bwDestroyIndexNode(bwRTreeNode_t *node)
Destroy an bwRTreeNode_t and all of its children.
Definition: bwValues.c:758
+
bwDestroyIndexNode
void bwDestroyIndexNode(bwRTreeNode_t *node)
Destroy an bwRTreeNode_t and all of its children.
Definition: bwValues.c:762
bwOverlapBlock_t
This structure holds the data blocks that overlap a given interval.
Definition: bwValues.h:53
bwSetPos
int bwSetPos(bigWigFile_t *fp, size_t pos)
Like fsetpos, but for local or remote bigWig files. This will set the file position indicator to the ...
Definition: bwRead.c:19
-
bwFinalize
int bwFinalize(bigWigFile_t *fp)
Finishes what's needed to write a bigWigFile Flushes the buffer, converts the index linked list to a ...
Definition: bwWrite.c:1203
-
bwDestroyIndex
void bwDestroyIndex(bwRTree_t *idx)
Frees space allocated by bwReadIndex There is generally little reason to use this, since end users should typically not need to run bwReadIndex themselves.
Definition: bwValues.c:779
-
bigWigFile_t
A structure that holds everything needed to access a bigWig file.
Definition: bigWig.h:203
-
bwReadIndex
bwRTree_t * bwReadIndex(bigWigFile_t *fp, uint64_t offset)
Reads a data index (either full data or a zoom level) from a bigWig file. There is little reason for ...
Definition: bwValues.c:786
+
bwFinalize
int bwFinalize(bigWigFile_t *fp)
Finishes what's needed to write a bigWigFile Flushes the buffer, converts the index linked list to a ...
Definition: bwWrite.c:1224
+
bwDestroyIndex
void bwDestroyIndex(bwRTree_t *idx)
Frees space allocated by bwReadIndex There is generally little reason to use this, since end users should typically not need to run bwReadIndex themselves.
Definition: bwValues.c:783
+
bigWigFile_t
A structure that holds everything needed to access a bigWig file.
Definition: bigWig.h:204
+
bwReadIndex
bwRTree_t * bwReadIndex(bigWigFile_t *fp, uint64_t offset)
Reads a data index (either full data or a zoom level) from a bigWig file. There is little reason for ...
Definition: bwValues.c:790
bwRTree_t
Definition: bwValues.h:36
bwTell
long bwTell(bigWigFile_t *fp)
Determine what the file position indicator say. This is equivalent to ftell for local or remote files...
Definition: bwRead.c:11
bwRead
size_t bwRead(void *data, size_t sz, size_t nmemb, bigWigFile_t *fp)
A local/remote version of fread. Reads data from either local or remote bigWig files.
Definition: bwRead.c:26
@@ -115,7 +115,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bwValues_8h.html b/docs/html/bwValues_8h.html index 31f7e7d..25a63ff 100644 --- a/docs/html/bwValues_8h.html +++ b/docs/html/bwValues_8h.html @@ -69,7 +69,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -134,7 +134,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/bwValues_8h_source.html b/docs/html/bwValues_8h_source.html index c33cc77..9e13801 100644 --- a/docs/html/bwValues_8h_source.html +++ b/docs/html/bwValues_8h_source.html @@ -70,7 +70,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -169,7 +169,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/classes.html b/docs/html/classes.html index 7038262..5e101f4 100644 --- a/docs/html/classes.html +++ b/docs/html/classes.html @@ -71,7 +71,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -102,7 +102,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/files.html b/docs/html/files.html index b1f3dcc..bb62e9b 100644 --- a/docs/html/files.html +++ b/docs/html/files.html @@ -70,7 +70,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -95,7 +95,7 @@
-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/functions.html b/docs/html/functions.html index a4f0b31..5012341 100644 --- a/docs/html/functions.html +++ b/docs/html/functions.html @@ -101,7 +101,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -468,7 +468,7 @@

- z -

-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/functions_vars.html b/docs/html/functions_vars.html index e492bbd..906d0c5 100644 --- a/docs/html/functions_vars.html +++ b/docs/html/functions_vars.html @@ -101,7 +101,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
@@ -468,7 +468,7 @@

- z -

-Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
diff --git a/docs/html/globals.html b/docs/html/globals.html index 0060601..43ca208 100644 --- a/docs/html/globals.html +++ b/docs/html/globals.html @@ -71,17 +71,21 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -91,7 +95,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -103,6 +107,13 @@
    Here is a list of all documented functions, variables, defines, enums, and typedefs with links to the documentation:
    +

    - a -

    + +

    - b -

    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_defs.html b/docs/html/globals_defs.html index 3c41503..0c3a24e 100644 --- a/docs/html/globals_defs.html +++ b/docs/html/globals_defs.html @@ -71,6 +71,7 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -80,7 +81,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -119,7 +120,7 @@
    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_enum.html b/docs/html/globals_enum.html index fceb84a..ac777c8 100644 --- a/docs/html/globals_enum.html +++ b/docs/html/globals_enum.html @@ -71,6 +71,7 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -80,7 +81,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -101,7 +102,7 @@
    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_eval.html b/docs/html/globals_eval.html index 23ab2a8..0eacb6b 100644 --- a/docs/html/globals_eval.html +++ b/docs/html/globals_eval.html @@ -69,8 +69,10 @@
  • All
  • Functions
  • Variables
    • +
  • Typedefs
  • Enumerations
  • Enumerator
    • +
  • Macros
    • @@ -79,7 +81,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Enumerations Enumerator Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -90,23 +92,41 @@
     
    -Generated on Wed Aug 5 2015 14:17:20 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_func.html b/docs/html/globals_func.html index cb9e94a..23f0d39 100644 --- a/docs/html/globals_func.html +++ b/docs/html/globals_func.html @@ -71,6 +71,7 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -86,7 +87,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -227,7 +228,7 @@

    - u -

    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_type.html b/docs/html/globals_type.html index 0486f1b..fda98d1 100644 --- a/docs/html/globals_type.html +++ b/docs/html/globals_type.html @@ -71,6 +71,7 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -80,7 +81,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -98,7 +99,7 @@
    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/globals_vars.html b/docs/html/globals_vars.html index 7863dae..ce20e16 100644 --- a/docs/html/globals_vars.html +++ b/docs/html/globals_vars.html @@ -71,6 +71,7 @@
  • Variables
  • Typedefs
  • Enumerations
    • +
  • Enumerator
  • Macros
    • @@ -80,7 +81,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -98,7 +99,7 @@
    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:30 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/index.html b/docs/html/index.html index fe8212f..5f720ba 100644 --- a/docs/html/index.html +++ b/docs/html/index.html @@ -64,7 +64,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -106,7 +106,7 @@

    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
    diff --git a/docs/html/md_README.html b/docs/html/md_README.html index 31e7f92..e344e21 100644 --- a/docs/html/md_README.html +++ b/docs/html/md_README.html @@ -63,7 +63,7 @@ onmouseover="return searchBox.OnSearchSelectShow()" onmouseout="return searchBox.OnSearchSelectHide()" onkeydown="return searchBox.OnSearchSelectKey(event)"> - All Data Structures Files Functions Variables Typedefs Enumerations Macros Pages + All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Pages
    @@ -274,7 +274,7 @@

    Example

    } bwIteratorDestroy(iter);

    A note on bigWig statistics

    -

    The results of min, max, and mean should be the same as those from BigWigSummary. stdev and coverage, however, may differ due to Kent's tools producing incorrect results (at least for coverage, though the same appears to be the case for stdev).

    +

    The results of min, max, and mean should be the same as those from BigWigSummary. stdev and coverage, however, may differ due to Kent's tools producing incorrect results (at least for coverage, though the same appears to be the case for stdev). The sum method doesn't exist in Kent's tools, so note that if zoom levels are used, that it will multiply the block average by the lesser of the number of bases covered in the block and the number of bases in a block overlapping the desired region.

    Python interface

    There are currently two python interfaces that make use of libBigWig: pyBigWig by me and bw-python by Brent Pederson. Those interested are encouraged to give both a try!

    Building without remote file access

    @@ -282,7 +282,7 @@

    Building without remote file access

    -Generated on Mon Jul 24 2017 09:40:02 for libBigWig by   +Generated on Mon Jan 8 2018 13:39:29 for libBigWig by   doxygen 1.8.6
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    @@ -86,7 +86,7 @@
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