vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq. vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
User-visible changes:
- use Myers diff instead of Patience diff when merging files with diff3
- improve got log -x documentation
- improve got ref -d documentation
- ensure that old commits remain referenced after rebase and histedit
- new got rebase -l option which lists past rebase operations
- new got histedit -l option which lists past histedit operations
ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file. SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
LLD currently fails:
ld: error: relocation refers to a discarded section: .rodata._ZN5boost6detail8function15functor_managerINS_9algorithm6detail13token_finderFINS4_10is_any_ofFIcEEEEE7managerERKNS1_15function_bufferERSA_NS1_30functor_manager_operation_typeEN4mpl_5bool_ILb0EEE
>>> defined in ../../archive_output_directory/libmysqlpump_lib.a(object_filter.cc.o)
>>> referenced by object_filter.cc
>>> object_filter.cc.o:(.got2+0x108) in archive ../../archive_output_directory/libmysqlpump_lib.a
ld: error: relocation refers to a discarded section: .rodata._ZN5boost6detail8function15functor_managerINS_9algorithm6detail13token_finderFINS4_10is_any_ofFIcEEEEE7managerERKNS1_15function_bufferERSA_NS1_30functor_manager_operation_typeEN4mpl_5bool_ILb0EEE
>>> defined in ../../archive_output_directory/libmysqlpump_lib.a(sql_formatter.cc.o)
>>> referenced by sql_formatter.cc
>>> sql_formatter.cc.o:(.got2+0x130) in archive ../../archive_output_directory/libmysqlpump_lib.a
ld: error: relocation refers to a discarded section: .rodata._ZN5boost6detail8function15functor_managerINS_9algorithm6detail13token_finderFINS4_10is_any_ofFIcEEEEE7managerERKNS1_15function_bufferERSA_NS1_30functor_manager_operation_typeEN4mpl_5bool_ILb0EEE
>>> defined in ../../archive_output_directory/libmysqlpump_lib.a(table.cc.o)
>>> referenced by table.cc
>>> table.cc.o:(.got2+0x50) in archive ../../archive_output_directory/libmysqlpump_lib.a
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
From ChangeLog: https://shotcut.org/blog/new-release-210321/
* Fixed <tractor> and blank considered missing and blocking export
* Added an Ignore button to the missing files error dialog in Export.
* Fixed black frames appearing in Slideshow Generator
* Fixed being able to use mouse wheel over Timeline and Keyframes zoom sliders
* Improved sound quality with small changes in Speed with Pitch Compensation or
Pitch audio filter (broke in v20.11).
* Fixed the Timeline clip audio waveform incorrect after adding transition by
dragging the clip left.
* Fixed repairing a project file opened using a network path on Windows.
* Fixed writing a raw FLAC file does not set its duration.
* Fixed an elided file name in clip Properties can become the clip name.
Deleteing patch integrated upstream: https://github.com/mltframework/shotcut/pull/1050
Reported by: portscout
[192/192] LINK gn
ERROR at //build/config/linux/pkg_config.gni:103:17: Script returned non-zero exit code.
pkgresult = exec_script(pkg_config_script, args, "value")
^----------
Package gbm was not found in the pkg-config search path.
Perhaps you should add the directory containing `gbm.pc'
to the PKG_CONFIG_PATH environment variable
Package 'gbm', required by 'virtual:world', not found
Could not run pkg-config.
See //third_party/minigbm/BUILD.gn:122:3: whence it was called.
pkg_config("libgbm") {
^---------------------
See //ui/gfx/linux/BUILD.gn:41:5: which caused the file to be included.
"//third_party/minigbm",
^----------------------
This commit should ensure that we have a htop package for 13.0-RELEASE
on non-x86 archs. When sysutils/lsof fails to build (and that
happens often enough) htop is skipped and we no longer have a package
for it. lsof is only used for htop's "list open files" view.
PR: 252279
- Fix DOCS build by disabling deny-warnings (rustc equivalent to
-Werror). Let's not fail the entire build just because a handful
of docs fail to build due to -D broken-intra-doc-links [0]
- Only install the host target docs. We otherwise waste time with
a rust-docs install-uninstall-install cycle for each additional
target during stage.
- Backport FreeBSD support for gimli, unbreak RUST_BACKTRACE, and
have useful stack traces with actual content again [1]
- While here also strip binaries under libexec/ and ack reading of
src/bootstrap/CHANGELOG.md (changelog-seen=2)
[0] https://github.com/rust-lang/rust/issues/76526
PR: 253557 [1]
Submitted by: jbeich [1]
