NEWS
Rhtslib 3.0.0
SIGNIFICANT USER-VISIBLE CHANGES
- Update htslib to 1.18 (was 1.15.1)
Rhtslib 2.2.0
- No significant changes in this version.
Rhtslib 2.0.0
SIGNIFICANT USER-VISIBLE CHANGES
- Update htslib to 1.15.1 (was 1.7)
Rhtslib 1.28.0
SIGNIFICANT USER-VISIBLE CHANGES
- Acknowledge site-wide or user-specified Makevars file if present.
Rhtslib 1.26.0
- No significant changes in this version.
Rhtslib 1.24.0
- No significant changes in this version.
Rhtslib 1.22.0
- No significant changes in this version.
Rhtslib 1.20.0
- No significant changes in this version.
Rhtslib 1.18.0
NEW FEATURES
- Compile HTSlib with libcurl enabled
- Support an installation path that contains whitespaces
SIGNIFICANT USER-VISIBLE CHANGES
- Switch from dynamic to static linking on all Unix-like systems (see
commit db1d8e17)
- Package now requires libbz2 & liblzma & libcurl (with header files),
and GNU make. This is declared in new SystemRequirements field.
BUG FIXES
- 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/
- Don't overwrite CPPFLAGS, CFLAGS, or LDFLAGS values set in
${R_HOME}/etc/Makeconf on Linux or Mac
Rhtslib 1.16.0
SIGNIFICANT USER-VISIBLE CHANGES
- Include various additional files from Samtools 1.7: bam_aux.c,
bam_endian.h, and bam_cat.c
- 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
- 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().
- Fix for Solaris: Do not build standalone executables (e.g. bgzip, tabix,
etc...). They're not needed and seem to cause problems on Solaris.
Rhtslib 1.14.0
SIGNIFICANT USER-VISIBLE CHANGES
- 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")
- 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"
- 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.
- 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.
- 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.
- 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
- 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.
Rhtslib 1.12.0
SIGNIFICANT USER-VISIBLE CHANGES
- The HTSlib C library was updated from version 1.1 to version 1.7.