[med-svn] [SCM] pysam branch, master, updated. upstream/0.3.1-8-gd3b27d0

[Charles Plessy]

The following commit has been merged in the master branch:
commit 5462ea03c0ad4b9349aa2034fee8ad4fa1803e9a
Author: Charles Plessy <plessy at debian.org>
Date:   Tue Feb 1 18:27:21 2011 +0900

    # Patch fixing upstream issue n°54.
    
    Description: pytype not defined for FloatType tags
    URL: http://code.google.com/p/pysam/issues/detail?id=54

diff --git a/debian/patches/issue-54 b/debian/patches/issue-54
new file mode 100644
index 0000000..81b16ff
--- /dev/null
+++ b/debian/patches/issue-54
@@ -0,0 +1,13 @@
+diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx
+index e94e0e6..39e136b 100644
+--- a/pysam/csamtools.pyx
++++ b/pysam/csamtools.pyx
+@@ -1599,7 +1599,7 @@ cdef class AlignedRead:
+                 for pytag, value in tags:
+                     t = type(value)
+                     if t == types.FloatType:
+-                        fmt = "<cccf"
++                        fmt, pytype = "<cccf", 'f'
+                     elif t == types.IntType:
+                         if value < 0:
+                             if value >= -127: fmt, pytype = "<cccb", 'c'
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9bc2b4c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+issue-54

-- 
interface for the SAM/BAM sequence alignment and mapping format