ncbi-vdb

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Import patches from FreeBSD port

4

This fork contains all the patches necessary for the FreeBSD port, and lays the foundation for porting to other BSDs. Since most of the OS checks were alphabetized, I also...

outpaddling

Enable Apple Silicon builds by adding `interfaces/cc/clang/aarch64`

1

In Homebrew, I was able to build v3.0.0 on Apple Silicon by adding an `interfaces/cc/clang/aarch64` (https://github.com/Homebrew/homebrew-core/pull/98654) linked from existing `interfaces/cc/gcc/arm64` I will note that trying to build with GCC failed...

cho-m

Error encountered while compiling for Arm platform

2

I got an error when compiling on arm platform ``` Consolidate compiler generated dependencies of target ncbi-bam [ 0%] Building C object libs/align/CMakeFiles/ncbi-bam.dir/bam.c.o In file included from /opt/installer/ncbi-vdb-3.0.0/interfaces/kfs/file-v2.h:35:0, from /opt/installer/ncbi-vdb-3.0.0/interfaces/kfs/file.h:39,...

hyacz

Some builtins that vdb uses are gcc-specific and don't compile with clang.

1

For example, ```__builtin_ia32_shufps``` and ```__builtin_ia32_shufpd``` are gcc-specific. You should replace them with primitives, ```_mm_shuffle_ps``` and ```_mm_shuffle_pd```, or better yet, you can use the SIMD library instead, like libsimdpp: https://github.com/p12tic/libsimdpp

yurivict

The gethostbyname*() and gethostbyaddr*() functions are deprecated as among other things they are not IPv6 ready

1

Applications should use getaddrinfo(3) and getnameinfo(3) instead. See also https://udrepper.livejournal.com/16116.html

V-Z

Reduce maximum memory usage while reading SRA data?

2

Using the C VDB API (and following the `fasterq-dump` utility strategy for accessing SRA records) for reading SRA data can consume a significant amount of RAM while reading an SRA...

jgans

FreeBSD compatibility patches

4

Upstreaming patches from the FreeBSD port.

yurivict

error: too few arguments to function ‘H5Oget_info_by_name3’

1

While following [the instructions](https://github.com/ncbi/ncbi-vdb/wiki/Building-and-Installing-from-Source) to compile from source, I faced this error after running `./configure && make`: Here is the colored version to help readability, the text of the error...

mmahmoudian

Reference Workflow for Fastq->SRA File (VDB Conversion)

2

Hello, Can anyone point me to a reference to the code that is used by the SRA project to convert from a user's submitted FASTQ files to the VDB/.sra format...

LRParser

Installs static libs instead of shared libs, for example lib/libncbi-vdb.a.2.11.0

5

Version 2.11.0 installs static libs instead of shared libs: ``` lib/libkdf5-static.a lib/libkdf5.a lib/libkdf5.a.2 lib/libkdf5.a.2.11.0 lib/libkdf5.so lib/libkdf5.so.2 lib/libkdf5.so.2.11.0 lib/libncbi-ngs-c++-static.a lib/libncbi-ngs-c++.a lib/libncbi-ngs-c++.a.2 lib/libncbi-ngs-c++.a.2.11.0 lib/libncbi-ngs-static.a lib/libncbi-ngs.a lib/libncbi-ngs.a.2 lib/libncbi-ngs.a.2.11.0 lib/libncbi-vdb-static.a lib/libncbi-vdb.a lib/libncbi-vdb.a.2 lib/libncbi-vdb.a.2.11.0 lib/libncbi-vdb.so...

yurivict