-
Notifications
You must be signed in to change notification settings - Fork 13
/
Copy pathNEWS
181 lines (115 loc) · 5.29 KB
/
NEWS
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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
CHANGES IN VERSION 3.2.0
------------------------
- No significant changes in this version.
CHANGES IN VERSION 3.0.0
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Update htslib to 1.18 (was 1.15.1)
CHANGES IN VERSION 2.2.0
-------------------------
- No significant changes in this version.
CHANGES IN VERSION 2.0.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Update htslib to 1.15.1 (was 1.7)
CHANGES IN VERSION 1.28.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Acknowledge site-wide or user-specified Makevars file if present.
CHANGES IN VERSION 1.26.0
-------------------------
- No significant changes in this version.
CHANGES IN VERSION 1.24.0
-------------------------
- No significant changes in this version.
CHANGES IN VERSION 1.22.0
-------------------------
- No significant changes in this version.
CHANGES IN VERSION 1.20.0
-------------------------
- No significant changes in this version.
CHANGES IN VERSION 1.18.0
-------------------------
NEW FEATURES
o Compile HTSlib with libcurl enabled
o Support an installation path that contains whitespaces
SIGNIFICANT USER-VISIBLE CHANGES
o Switch from dynamic to static linking on all Unix-like systems (see
commit db1d8e17)
o Package now requires libbz2 & liblzma & libcurl (with header files),
and GNU make. This is declared in new SystemRequirements field.
BUG FIXES
o Use preprocessor flag -D_FILE_OFFSET_BITS=64. This addresses nasty
problem with big files that get truncated on Windows. See
https://support.bioconductor.org/p/124568/
o Don't overwrite CPPFLAGS, CFLAGS, or LDFLAGS values set in
${R_HOME}/etc/Makeconf on Linux or Mac
CHANGES IN VERSION 1.16.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Include various additional files from Samtools 1.7: bam_aux.c,
bam_endian.h, and bam_cat.c
o Add C function faidx_fetch_seq_forced_lower() to the HTSlib code.
This is an alternative to HTSlib C function faidx_fetch_seq(), with the
following difference: if coordinates are outside the actual sequence,
write N's, rather than adjusting the start,end.
Used in the seqbias package (and originally written by seqbias' author
and maintainer, Daniel Jones).
BUG FIXES
o Fix long-standing kvsprintf() bug on Windows. This low-level bug was
responsible for breaking "scan_bcf_header" .Call entry point in
Rsamtools, which in turn was responsible for the infamous
'invalid class "VCFHeader" object' bug in VariantAnnotation::readVcf().
o Fix for Solaris: Do not build standalone executables (e.g. bgzip, tabix,
etc...). They're not needed and seem to cause problems on Solaris.
CHANGES IN VERSION 1.14.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Include the test data files from htslib-1.7/test
For convenience, the .sam, .bam, .vcf, .bcf, .cram, .fa, .fa.fai, .gff,
and .bed files located under htslib-1.7/test now are also included in
the package (under ${R_PACKAGE_DIR}/testdata). They can be accessed with
something like:
system.file(package="Rhtslib", "testdata", "ce#1.sam")
or:
system.file(package="Rhtslib", "testdata", "tabix", "vcf_file.vcf")
o Change installation folder of htslib header files. HTSlib header files
now get installed in ${R_PACKAGE_DIR}/include/htslib instead of
${R_PACKAGE_DIR}/include so C/C++ code that needs to include them
now should use directives like:
#include "htslib/hts.h"
#include "htslib/sam.h"
#include "htslib/bgzf.h"
instead of:
#include "hts.h"
#include "sam.h"
#include "bgzf.h"
o Include various .h and .c files from Samtools 1.7 (in
${R_PACKAGE_DIR}/include). These files come from the top-level folder
of the Samtools source tree. See Rhtslib/inst/include/README for more
information.
o Include textutils_internal.h and hts_internal.h from HTSlib 1.7 (in
${R_PACKAGE_DIR}/include). These files come from the top-level folder
of the HTSlib source tree.
o Add C function faidx_fetch_seq2() to the HTSlib code. This is an
alternative to HTSlib C function faidx_fetch_seq(), with the following
differences:
1) writes the incoming sequence to user-supplied 'out' buffer,
2) doesn't write the terminating null byte ('\0'),
3) properly handles 0-length sequences,
4) returns the number of bytes written; -1 on failure.
It will be used in Rsamtools::scanFa() when Rsamtools gets migrated
to Rhtslib. It allows the incoming sequences to be loaded directly
into the DNAStringSet object to return.
o Add C function hts_idx_get_n() to the HTSlib code. This function will
be used in Rsamtools::idxstatsBam() when Rsamtools gets migrated
to Rhtslib.
BUG FIXES
o Simplify PKG_LIBS on Mac. There should be no need to use linker options
-lz -lm -lbz2 -llzma -lcurl and -lpthread on Mac when making the package
shared object because we link against **static** library libhts.a on
this platform.
CHANGES IN VERSION 1.12.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The HTSlib C library was updated from version 1.1 to version 1.7.