[med-svn] [Git][med-team/pybigwig][upstream] New upstream version 0.3.17

[Diane Trout]

Diane Trout pushed to branch upstream at Debian Med / pybigwig


Commits:
b0527a23 by Diane Trout at 2019-09-05T04:25:21Z
New upstream version 0.3.17
- - - - -


4 changed files:

- README.md
- pyBigWig.c
- pyBigWig.h
- setup.py


Changes:

=====================================
README.md
=====================================
@@ -144,9 +144,6 @@ For the sake of consistency with other tools, pyBigWig adopts this same methodol
     0.22213841940688142
     >>> bw.stats('chr1', 89294, 91629, exact=True)
     [0.22213841940688142]
-Additionally, `values()` can directly output a numpy vector:
-
-    >>> bw = bw.open("
 
 ## Retrieve values for individual bases in a range
 
@@ -218,6 +215,8 @@ By default, up to 10 "zoom levels" are constructed for bigWig files. You can cha
 
     >>> bw.addHeader([("chr1", 1000000), ("chr2", 1500000)], maxZooms=0)
 
+If you set `maxTooms=0`, please note that IGV and many other tools WILL NOT WORK as they assume that at least one zoom level will be present. You are advised to use the default unless you do not expect the bigWig files to be used by other packages.
+
 ## Adding entries to a bigWig file
 
 Assuming you've opened a file for writing and added a header, you can then add entries. Note that the entries **must** be added in order, as bigWig files always contain ordered intervals. There are three formats that bigWig files can use internally to store entries. The most commonly observed format is identical to a [bedGraph](https://genome.ucsc.edu/goldenpath/help/bedgraph.html) file:


=====================================
pyBigWig.c
=====================================
@@ -276,6 +276,10 @@ static PyObject *pyBwGetHeader(pyBigWigFile_t *self, PyObject *args) {
         PyErr_SetString(PyExc_RuntimeError, "The bigWig file handle is not opened!");
         return NULL;
     }
+    if(bw->isWrite == 1) {
+        PyErr_SetString(PyExc_RuntimeError, "The header cannot be accessed in files opened for writing!");
+        return NULL;
+    }
 
     ret = PyDict_New();
     val = PyLong_FromUnsignedLong(bw->hdr->version);
@@ -321,6 +325,11 @@ static PyObject *pyBwGetChroms(pyBigWigFile_t *self, PyObject *args) {
         return NULL;
     }
 
+    if(bw->isWrite == 1) {
+        PyErr_SetString(PyExc_RuntimeError, "Chromosomes cannot be accessed in files opened for writing!");
+        return NULL;
+    }
+
     if(!(PyArg_ParseTuple(args, "|s", &chrom)) || !chrom) {
         ret = PyDict_New();
         for(i=0; i<bw->cl->nKeys; i++) {
@@ -380,6 +389,11 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw
         return NULL;
     }
 
+    if(bw->isWrite == 1) {
+        PyErr_SetString(PyExc_RuntimeError, "Statistics cannot be accessed in files opened for writing!");
+        return NULL;
+    }
+
     if(bw->type == 1) {
         PyErr_SetString(PyExc_RuntimeError, "bigBed files have no statistics!");
         return NULL;
@@ -621,6 +635,11 @@ static PyObject *pyBwGetIntervals(pyBigWigFile_t *self, PyObject *args, PyObject
         return NULL;
     }
 
+    if(bw->isWrite == 1) {
+        PyErr_SetString(PyExc_RuntimeError, "Intervals cannot be accessed in files opened for writing!");
+        return NULL;
+    }
+
     if(bw->type == 1) {
         PyErr_SetString(PyExc_RuntimeError, "bigBed files have no intervals! Use 'entries()' instead.");
         return NULL;
@@ -724,7 +743,7 @@ int PyString_Check(PyObject *obj) {
 
 //I don't know what happens if PyBytes_AsString(NULL) is used...
 char *PyString_AsString(PyObject *obj) {
-    return PyBytes_AsString(PyUnicode_AsASCIIString(obj));
+    return PyUnicode_AsUTF8(obj);
 }
 #endif
 


=====================================
pyBigWig.h
=====================================
@@ -2,7 +2,7 @@
 #include <structmember.h>
 #include "bigWig.h"
 
-#define pyBigWigVersion "0.3.16"
+#define pyBigWigVersion "0.3.17"
 
 typedef struct {
     PyObject_HEAD


=====================================
setup.py
=====================================
@@ -62,7 +62,7 @@ module1 = Extension('pyBigWig',
                     include_dirs = include_dirs)
 
 setup(name = 'pyBigWig',
-       version = '0.3.16',
+       version = '0.3.17',
        description = 'A package for accessing bigWig files using libBigWig',
        author = "Devon P. Ryan",
        author_email = "ryan at ie-freiburg.mpg.de",



View it on GitLab: https://salsa.debian.org/med-team/pybigwig/commit/b0527a23da9c286bb34097630e9af49dbb12d8da

-- 
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/commit/b0527a23da9c286bb34097630e9af49dbb12d8da
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190905/6a3a6ea3/attachment-0001.html>