1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
=============
Release notes
=============
Release 0.7.7
=============
* added Fastafile.references, .nreferences and .lengths
* tabix_iterator now uses kseq.h for python 2.7
Release 0.7.6
=============
* added inferred_length property
* issue 122: MACOSX getline missing, now it works?
* seq and qual can be set None
* added Fastqfile
Release 0.7.5
=============
* switch to samtools 0.1.19
* issue 122: MACOSX getline missing
* issue 130: clean up tempfiles
* various other bugfixes
Release 0.7.4
=============
* further bugfixes to setup.py and package layout
Release 0.7.3
=============
* further bugfixes to setup.py
* upgraded distribute_setup.py to 0.6.34
Release 0.7.2
=============
* bugfix in installer - failed when cython not present
* changed installation locations of shared libraries
Release 0.7.1
=============
* bugfix: missing PP tag PG records in header
* added pre-built .c files to distribution
Release 0.7
===========
* switch to tabix 0.2.6
* added cigarstring field
* python3 compatibility
* added B tag handling
* added check_sq and check_header options to Samfile.__init__
* added lazy GTF parsing to tabix
* reworked support for VCF format parsing
* bugfixes
Release 0.6
===========
* switch to samtools 0.1.18
* various bugfixes
* removed references to deprecated 'samtools pileup' functionality
* AlignedRead.tags now returns an empty list if there are no tags.
* added pnext, rnext and tlen
Release 0.5
===========
* switch to samtools 0.1.16 and tabix 0.2.5
* improved tabix parsing, added vcf support
* re-organized code to permit linking againts pysam
* various bugfixes
* added Samfile.positions and Samfile.overlap
Release 0.4
===========
* switch to samtools 0.1.12a and tabix 0.2.3
* added snp and indel calling.
* switch from pyrex to cython
* changed handling of samtools stderr
* various bugfixes
* added Samfile.count and Samfile.mate
* deprecated AlignedRead.rname, added AlignedRead.tid
Release 0.3
===========
* switch to samtools 0.1.8
* added support for tabix files
* numerous bugfixes including
* permit simultaneous iterators on the same file
* working access to remote files
|
