Merge pull request #30 from seqeralabs/staden_io_lib

Staden io lib

recipes/staden_io_lib/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+./configure --prefix=${PREFIX} --with-libdeflate=${PREFIX}
+make
+make install

recipes/staden_io_lib/fixhwcap.patch

@@ -0,0 +1,22 @@
+diff --git a/htscodecs/htscodecs/rANS_static4x16pr.c b/htscodecs/htscodecs/rANS_static4x16pr.c
+index 07ee54b..a2b4ac0 100644
+--- a/htscodecs/htscodecs/rANS_static4x16pr.c
++++ b/htscodecs/htscodecs/rANS_static4x16pr.c
+@@ -1018,7 +1018,7 @@ static inline int have_neon() {
+ #if defined(__linux__) && defined(__arm__)
+     return (getauxval(AT_HWCAP) & HWCAP_NEON) != 0;
+ #elif defined(__linux__) && defined(__aarch64__)
+-    return (getauxval(AT_HWCAP) & HWCAP_ASIMD) != 0;
++    return (getauxval(AT_HWCAP) & 2) != 0;
+ #elif defined(__APPLE__)
+     return 1;
+ #elif defined(__FreeBSD__) && defined(__arm__)
+@@ -1028,7 +1028,7 @@ static inline int have_neon() {
+ #elif defined(__FreeBSD__) && defined(__aarch64__)
+     u_long cap;
+     if (elf_aux_info(AT_HWCAP, &cap, sizeof cap) != 0) return 0;
+-    return (cap & HWCAP_ASIMD) != 0;
++    return (cap & 2) != 0;
+ #elif defined(_WIN32)
+     return IsProcessorFeaturePresent(PF_ARM_V8_INSTRUCTIONS_AVAILABLE) != 0;
+ #else

recipes/staden_io_lib/meta.yaml

@@ -0,0 +1,46 @@
+{% set name = "staden_io_lib" %}
+{% set version = "1.14.15" %}
+{% set hash = "20814c4365e1e2fe6630fb11d0df370dec4c5688af3871de7f1cb0129671401e" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-15/io_lib-1.14.15.tar.gz
+  sha256: {{ hash }}
+  patches:
+    - fixhwcap.patch
+
+build:
+  number: 7
+  skip: True # [osx]
+  run_exports:
+    - {{ pin_subpackage('staden_io_lib', max_pin='x.x') }}
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+  host:
+    - bzip2
+    - zlib
+    - xz
+    - curl
+    - libdeflate
+  run:
+    - bzip2
+    - zlib
+    - xz
+    - curl
+    - libdeflate
+
+test:
+  commands:
+    - "cram_size 2>&1 | grep 'Usage: cram_size'"
+
+about:
+  home: https://github.com/jkbonfield/io_lib/
+  license: BSD
+  license_file: COPYRIGHT
+  summary: 'Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM'