[med-svn] [Git][med-team/libbigwig][upstream] 2 commits: New upstream version 0.4.4+dfsg
Steffen Möller
gitlab at salsa.debian.org
Thu Dec 5 11:52:59 GMT 2019
Steffen Möller pushed to branch upstream at Debian Med / libbigwig
Commits:
7755c72f by Steffen Moeller at 2019-12-05T11:34:45Z
New upstream version 0.4.4+dfsg
- - - - -
c41a8763 by Steffen Moeller at 2019-12-05T11:51:02Z
New upstream version 0.4.4+dfsg
- - - - -
5 changed files:
- README.md
- bigWig.h
- bwRead.c
- bwValues.c
- io.c
Changes:
=====================================
README.md
=====================================
@@ -2,154 +2,160 @@
A C library for reading/parsing local and remote bigWig and bigBed files. While Kent's source code is free to use for these purposes, it's really inappropriate as library code since it has the unfortunate habit of calling `exit()` whenever there's an error. If that's then used inside of something like python then the python interpreter gets killed. This library is aimed at resolving these sorts of issues and should also use more standard things like curl and has a friendlier license to boot.
-Documentation is automatically generated by doxygen and can be found under `docs/html` or online [here](https://cdn.rawgit.com/dpryan79/libBigWig/master/docs/html/index.html).
+Documentation is automatically generated by doxygen and can be found under [`docs/html`](/docs/html) or online [here](https://cdn.rawgit.com/dpryan79/libBigWig/master/docs/html/index.html).
# Example
-The only functions and structures that end users need to care about are in "bigWig.h". Below is a commented example. You can see the files under `test/` for further examples.
-
- #include "bigWig.h"
- int main(int argc, char *argv[]) {
- bigWigFile_t *fp = NULL;
- bwOverlappingIntervals_t *intervals = NULL;
- double *stats = NULL;
- if(argc != 2) {
- fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);
- return 1;
- }
-
- //Initialize enough space to hold 128KiB (1<<17) of data at a time
- if(bwInit(1<<17) != 0) {
- fprintf(stderr, "Received an error in bwInit\n");
- return 1;
- }
-
- //Open the local/remote file
- fp = bwOpen(argv[1], NULL, "r");
- if(!fp) {
- fprintf(stderr, "An error occured while opening %s\n", argv[1]);
- return 1;
- }
-
- //Get values in a range (0-based, half open) without NAs
- intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 0);
- bwDestroyOverlappingIntervals(intervals); //Free allocated memory
-
- //Get values in a range (0-based, half open) with NAs
- intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 1);
- bwDestroyOverlappingIntervals(intervals); //Free allocated memory
-
- //Get the full intervals that overlap
- intervals = bwGetOverlappingIntervals(fp, "chr1", 10000000, 10000100);
- bwDestroyOverlappingIntervals(intervals);
-
- //Get an example statistic - standard deviation
- //We want ~4 bins in the range
- stats = bwStats(fp, "chr1", 10000000, 10000100, 4, dev);
- if(stats) {
- printf("chr1:10000000-10000100 std. dev.: %f %f %f %f\n", stats[0], stats[1], stats[2], stats[3]);
- free(stats);
- }
-
- bwClose(fp);
- bwCleanup();
- return 0;
+The only functions and structures that end users need to care about are in "bigWig.h". Below is a commented example. You can see the files under [`test/`](./test/) for further examples.
+
+```c
+#include "bigWig.h"
+int main(int argc, char *argv[]) {
+ bigWigFile_t *fp = NULL;
+ bwOverlappingIntervals_t *intervals = NULL;
+ double *stats = NULL;
+ if(argc != 2) {
+ fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);
+ return 1;
+ }
+
+ //Initialize enough space to hold 128KiB (1<<17) of data at a time
+ if(bwInit(1<<17) != 0) {
+ fprintf(stderr, "Received an error in bwInit\n");
+ return 1;
+ }
+
+ //Open the local/remote file
+ fp = bwOpen(argv[1], NULL, "r");
+ if(!fp) {
+ fprintf(stderr, "An error occured while opening %s\n", argv[1]);
+ return 1;
+ }
+
+ //Get values in a range (0-based, half open) without NAs
+ intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 0);
+ bwDestroyOverlappingIntervals(intervals); //Free allocated memory
+
+ //Get values in a range (0-based, half open) with NAs
+ intervals = bwGetValues(fp, "chr1", 10000000, 10000100, 1);
+ bwDestroyOverlappingIntervals(intervals); //Free allocated memory
+
+ //Get the full intervals that overlap
+ intervals = bwGetOverlappingIntervals(fp, "chr1", 10000000, 10000100);
+ bwDestroyOverlappingIntervals(intervals);
+
+ //Get an example statistic - standard deviation
+ //We want ~4 bins in the range
+ stats = bwStats(fp, "chr1", 10000000, 10000100, 4, dev);
+ if(stats) {
+ printf("chr1:10000000-10000100 std. dev.: %f %f %f %f\n", stats[0], stats[1], stats[2], stats[3]);
+ free(stats);
}
+ bwClose(fp);
+ bwCleanup();
+ return 0;
+}
+```
+
## Writing example
N.B., creation of bigBed files is not supported (there are no plans to change this).
-Below is an example of how to write bigWig files. You can also find this file under `test/exampleWrite.c`. Unlike with Kent's tools, you can create bigWig files entry by entry without needing an intermediate wiggle or bedGraph file. Entries in bigWig files are stored in blocks with each entry in a block referring to the same chromosome and having the same type, of which there are three (see the [wiggle specification](http://genome.ucsc.edu/goldenpath/help/wiggle.html) for more information on this).
-
- #include "bigWig.h"
-
- int main(int argc, char *argv[]) {
- bigWigFile_t *fp = NULL;
- char *chroms[] = {"1", "2"};
- char *chromsUse[] = {"1", "1", "1"};
- uint32_t chrLens[] = {1000000, 1500000};
- uint32_t starts[] = {0, 100, 125,
- 200, 220, 230,
- 500, 600, 625,
- 700, 800, 850};
- uint32_t ends[] = {5, 120, 126,
- 205, 226, 231};
- float values[] = {0.0f, 1.0f, 200.0f,
- -2.0f, 150.0f, 25.0f,
- 0.0f, 1.0f, 200.0f,
- -2.0f, 150.0f, 25.0f,
- -5.0f, -20.0f, 25.0f,
- -5.0f, -20.0f, 25.0f};
-
- if(bwInit(1<<17) != 0) {
- fprintf(stderr, "Received an error in bwInit\n");
- return 1;
- }
-
- fp = bwOpen("example_output.bw", NULL, "w");
- if(!fp) {
- fprintf(stderr, "An error occurred while opening example_output.bw for writingn\n");
- return 1;
- }
-
- //Allow up to 10 zoom levels, though fewer will be used in practice
- if(bwCreateHdr(fp, 10)) goto error;
-
- //Create the chromosome lists
- fp->cl = bwCreateChromList(chroms, chrLens, 2);
- if(!fp->cl) goto error;
-
- //Write the header
- if(bwWriteHdr(fp)) goto error;
+Below is an example of how to write bigWig files. You can also find this file under [`test/exampleWrite.c`](test/exampleWrite.c). Unlike with Kent's tools, you can create bigWig files entry by entry without needing an intermediate wiggle or bedGraph file. Entries in bigWig files are stored in blocks with each entry in a block referring to the same chromosome and having the same type, of which there are three (see the [wiggle specification](http://genome.ucsc.edu/goldenpath/help/wiggle.html) for more information on this).
+
+```c
+#include "bigWig.h"
+
+int main(int argc, char *argv[]) {
+ bigWigFile_t *fp = NULL;
+ char *chroms[] = {"1", "2"};
+ char *chromsUse[] = {"1", "1", "1"};
+ uint32_t chrLens[] = {1000000, 1500000};
+ uint32_t starts[] = {0, 100, 125,
+ 200, 220, 230,
+ 500, 600, 625,
+ 700, 800, 850};
+ uint32_t ends[] = {5, 120, 126,
+ 205, 226, 231};
+ float values[] = {0.0f, 1.0f, 200.0f,
+ -2.0f, 150.0f, 25.0f,
+ 0.0f, 1.0f, 200.0f,
+ -2.0f, 150.0f, 25.0f,
+ -5.0f, -20.0f, 25.0f,
+ -5.0f, -20.0f, 25.0f};
- //Some example bedGraph-like entries
- if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
- //We can continue appending similarly formatted entries
- //N.B. you can't append a different chromosome (those always go into different
- if(bwAppendIntervals(fp, starts+3, ends+3, values+3, 3)) goto error;
-
- //Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block
- if(bwAddIntervalSpans(fp, "1", starts+6, 20, values+6, 3)) goto error;
- //We can continue appending similarly formatted entries
- if(bwAppendIntervalSpans(fp, starts+9, values+9, 3)) goto error;
-
- //Add a new block of fixed-step entries
- if(bwAddIntervalSpanSteps(fp, "1", 900, 20, 30, values+12, 3)) goto error;
- //The start is then 760, since that's where the previous step ended
- if(bwAppendIntervalSpanSteps(fp, values+15, 3)) goto error;
-
- //Add a new chromosome
- chromsUse[0] = "2";
- chromsUse[1] = "2";
- chromsUse[2] = "2";
- if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
-
- //Closing the file causes the zoom levels to be created
- bwClose(fp);
- bwCleanup();
-
- return 0;
-
- error:
- fprintf(stderr, "Received an error somewhere!\n");
- bwClose(fp);
- bwCleanup();
+ if(bwInit(1<<17) != 0) {
+ fprintf(stderr, "Received an error in bwInit\n");
return 1;
}
+ fp = bwOpen("example_output.bw", NULL, "w");
+ if(!fp) {
+ fprintf(stderr, "An error occurred while opening example_output.bw for writingn\n");
+ return 1;
+ }
+
+ //Allow up to 10 zoom levels, though fewer will be used in practice
+ if(bwCreateHdr(fp, 10)) goto error;
+
+ //Create the chromosome lists
+ fp->cl = bwCreateChromList(chroms, chrLens, 2);
+ if(!fp->cl) goto error;
+
+ //Write the header
+ if(bwWriteHdr(fp)) goto error;
+
+ //Some example bedGraph-like entries
+ if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
+ //We can continue appending similarly formatted entries
+ //N.B. you can't append a different chromosome (those always go into different
+ if(bwAppendIntervals(fp, starts+3, ends+3, values+3, 3)) goto error;
+
+ //Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block
+ if(bwAddIntervalSpans(fp, "1", starts+6, 20, values+6, 3)) goto error;
+ //We can continue appending similarly formatted entries
+ if(bwAppendIntervalSpans(fp, starts+9, values+9, 3)) goto error;
+
+ //Add a new block of fixed-step entries
+ if(bwAddIntervalSpanSteps(fp, "1", 900, 20, 30, values+12, 3)) goto error;
+ //The start is then 760, since that's where the previous step ended
+ if(bwAppendIntervalSpanSteps(fp, values+15, 3)) goto error;
+
+ //Add a new chromosome
+ chromsUse[0] = "2";
+ chromsUse[1] = "2";
+ chromsUse[2] = "2";
+ if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
+
+ //Closing the file causes the zoom levels to be created
+ bwClose(fp);
+ bwCleanup();
+
+ return 0;
+
+error:
+ fprintf(stderr, "Received an error somewhere!\n");
+ bwClose(fp);
+ bwCleanup();
+ return 1;
+}
+```
+
# Testing file types
As of version 0.3.0, this library supports accessing bigBed files, which are related to bigWig files. Applications that need to support both bigWig and bigBed input can use the `bwIsBigWig` and `bbIsBigBed` functions to determine if their inputs are bigWig/bigBed files:
- ...code...
- if(bwIsBigWig(input_file_name, NULL)) {
- //do something
- } else if(bbIsBigBed(input_file_name, NULL)) {
- //do something else
- } else {
- //handle unknown input
- }
+```c
+...code...
+if(bwIsBigWig(input_file_name, NULL)) {
+ //do something
+} else if(bbIsBigBed(input_file_name, NULL)) {
+ //do something else
+} else {
+ //handle unknown input
+}
+```
Note that these two functions rely on the "magic number" at the beginning of each file, which differs between bigWig and bigBed files.
@@ -220,12 +226,14 @@ Regardless of whether a bigWig or bigBed file is being used, the `bwIteratorNext
A full example is provided in `tests/testIterator.c`, but a small example of iterating over all bigWig intervals in `chr1:0-10000000` in chunks of 5 blocks follows:
- iter = bwOverlappingIntervalsIterator(fp, "chr1", 0, 10000000, 5);
- while(iter->data) {
- //Do stuff with iter->intervals
- iter = bwIteratorNext(iter);
- }
- bwIteratorDestroy(iter);
+```c
+iter = bwOverlappingIntervalsIterator(fp, "chr1", 0, 10000000, 5);
+while(iter->data) {
+ //Do stuff with iter->intervals
+ iter = bwIteratorNext(iter);
+}
+bwIteratorDestroy(iter);
+```
# A note on bigWig statistics
=====================================
bigWig.h
=====================================
@@ -53,7 +53,7 @@ extern "C" {
/*!
* The library version number
*/
-#define LIBBIGWIG_VERSION 0.4.2
+#define LIBBIGWIG_VERSION 0.4.4
/*!
* If 1, then this library was compiled with remote file support.
=====================================
bwRead.c
=====================================
@@ -73,7 +73,7 @@ static bwZoomHdr_t *bwReadZoomHdrs(bigWigFile_t *bw) {
return NULL;
}
uint64_t *indexOffset = malloc(sizeof(uint64_t) * bw->hdr->nLevels);
- if(!dataOffset) {
+ if(!indexOffset) {
free(zhdr);
free(level);
free(dataOffset);
=====================================
bwValues.c
=====================================
@@ -33,7 +33,7 @@ static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) {
return NULL;
}
- node = malloc(sizeof(bwRTree_t));
+ node = calloc(1, sizeof(bwRTree_t));
if(!node) return NULL;
if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
=====================================
io.c
=====================================
@@ -133,7 +133,7 @@ CURLcode urlSeek(URL_t *URL, size_t pos) {
#ifndef NOCURL
} else {
//If the location is covered by the buffer then don't seek!
- if(pos < URL->filePos || pos >= URL->filePos+URL->bufSize) {
+ if(pos < URL->filePos || pos >= URL->filePos+URL->bufLen) {
URL->filePos = pos;
URL->bufLen = 0; //Otherwise, filePos will get incremented on the next read!
URL->bufPos = 0;
View it on GitLab: https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807
--
View it on GitLab: https://salsa.debian.org/med-team/libbigwig/compare/15d08c7c90f241f84077c5714282782fd6b9a0b6...c41a87633c9cc5b699861162ee3312d084b2f807
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