biology/kallisto: Update to 0.50.1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases


(bacon)

$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.1 2023/11/04 14:35:07 bacon Exp $

# Portability

--- ext/bifrost/CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
+++ ext/bifrost/CMakeLists.txt
@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
 # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
 SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
 SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
-# Enable architecture optimizations
-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
-# Enable AVX2 instructions
-SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
+SET(CMAKE_VERBOSE_MAKEFILE "ON")
 
 # Set some default compile flags
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 
-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
-
-
 #check if we are on arm64 and apple, if so, disable AVX2
 if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
 	message("Disabling AVX2 instructions on arm64")
@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
 	message("Disabling native architecture compilation (including AVX2)")
 else(COMPILATION_ARCH MATCHES "OFF")
 	message("Compilation architecture: ${COMPILATION_ARCH}")
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
 endif(COMPILATION_ARCH MATCHES "OFF")
 
 if(ENABLE_AVX2 MATCHES "OFF")
@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
 		set(CMAKE_EXE_LINKER_FLAGS "-pg")
 	else(CMAKE_BUILD_TYPE MATCHES Profile)
 		message("Build type: Release")
-		add_compile_options(-O3)
+		add_compile_options(-O2)
 	endif(CMAKE_BUILD_TYPE MATCHES Profile) 
 endif(CMAKE_BUILD_TYPE MATCHES Debug)
 

$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $

# vfscanf() not found on NetBSD 9

--- ext/bifrost/src/BitContainer.cpp.orig	2023-11-01 12:46:19.000000000 +0000
+++ ext/bifrost/src/BitContainer.cpp
@@ -1,3 +1,4 @@
+#include <cstdio>
 #include "BitContainer.hpp"
 
 BitContainer::BitContainer() : setBits(localBitVector) {}

$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $

# vfscanf() not found on NetBSD 9

--- ext/bifrost/src/ColorSet.cpp.orig	2023-11-03 12:48:11.435933052 +0000
+++ ext/bifrost/src/ColorSet.cpp
@@ -1,3 +1,4 @@
+#include <cstdio>
 #include "ColorSet.hpp"
 
 UnitigColors::UnitigColors() : setBits(localBitVector) {}

$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.1 2023/11/04 14:35:07 bacon Exp $

# Use native popcnt

--- ext/bifrost/src/libpopcnt.h.orig	2023-07-24 12:34:08.037669065 +0000
+++ ext/bifrost/src/libpopcnt.h
@@ -32,6 +32,8 @@
 #ifndef LIBPOPCNT_H
 #define LIBPOPCNT_H
 
+#ifndef __NetBSD__
+
 #include <stdint.h>
 
 #ifndef __has_builtin
@@ -584,4 +586,6 @@ static inline uint64_t popcnt(const void
 
 #endif
 
+#endif /* NetBSD */
+
 #endif /* LIBPOPCNT_H */

$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.1 2023/11/04 14:35:07 bacon Exp $

# Portability

--- ext/bifrost/src/strict_fstream.hpp.orig	2023-06-27 10:45:00.000000000 +0000
+++ ext/bifrost/src/strict_fstream.hpp
@@ -64,7 +64,7 @@ static std::string strerror()
     } else {
         return "Unknown error (" + std::to_string(err_num) + ")";
     }
-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__)
+#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) || defined(__NetBSD__)
 // XSI-compliant strerror_r()
     const int err_num = errno; // See above
     if (strerror_r(err_num, buff.data(), buff.size()) == 0) {

$NetBSD: patch-src_Bootstrap.h,v 1.1 2023/11/04 14:35:07 bacon Exp $

# Portability

--- src/Bootstrap.h.orig	2020-04-01 16:56:42 UTC
+++ src/Bootstrap.h
@@ -1,6 +1,7 @@
 #ifndef KALLISTO_BOOTSTRAP_H
 #define KALLISTO_BOOTSTRAP_H
 
+#include <sys/types.h>
 #include <mutex>
 #include <thread>
 

$NetBSD: patch-src_main.cpp,v 1.1 2023/11/04 14:35:07 bacon Exp $

# Portability

--- src/main.cpp.orig	2023-11-01 12:46:19.000000000 +0000
+++ src/main.cpp
@@ -11,6 +11,7 @@
 #include <limits>
 
 #include <cstdio>
+#include <unistd.h>	// rmdir()
 
 #include "common.h"
 #include "ProcessReads.h"