Merge branch 'patch_pointers' into 'dev'

Initialize pointers to NULL

See merge request epi2melabs/fastcat!37

.gitlab-ci.yml

@@ -76,3 +76,14 @@ conda-mac-arm:
     extends: .deploy-conda-mac-arm
     before_script:
         - *before-script
+
+test-conda-arm:
+    stage: test
+    extends: .deploy-conda-linux-arm
+    variables:
+        UPLOAD: "no"
+    before_script:
+        - *prep-image
+        - *before-script
+    rules:
+    - if: $CI_COMMIT_BRANCH != null

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "htslib"]
 	path = htslib
-	url = https://github.com/samtools/htslib.git
+	url = https://github.com/samtools/htslib.git

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.14.1]
+### Fixed
+- Missing compilation of conda aarch64 package
+
 ## [v0.14.0]
 ### Added
 - `bamstats --duplex` option allows to count the number of duplex reads and 

Makefile

@@ -27,7 +27,7 @@ endif
 
 # we can't do pedantic because min/max macros lead to:
 #     "ISO C forbids braced-groups within expressions [-Werror=pedantic]"
-ifeq ($(shell $(CC) --version | grep clag | wc -l), 0)
+ifeq ($(shell $(CC) --version | grep clang | wc -l), 0)
     WARNINGS = -Werror -Wall -Wextra -Wno-incompatible-pointer-types
 else
     WARNINGS = -Werror -Wall -Wextra -Wpedantic -Wno-language-extension-token -Wno-gnu-statement-expression -Wno-incompatible-function-pointer-types

conda/meta.yaml

@@ -14,9 +14,9 @@ requirements:
     host:
         - argp-standalone # [osx]
         # linked to all the same stuff as bioconda builds
-        - bioconda::htslib
+        - nanoporetech::htslib =1.16
     run:
-        - bioconda::htslib
+        - nanoporetech::htslib
 test:
     commands:
         fastcat --help

src/bamindex/index.c

@@ -14,7 +14,7 @@ char* generate_index_filename(const char* input_bam, const char* input_index) {
     char* out_fn;
 
     if(input_index != NULL) {
-        out_fn = malloc(strlen(input_index));
+        out_fn = calloc(sizeof(char), strlen(input_index) + 1);
         if(out_fn == NULL) {
             exit(EXIT_FAILURE);
         }

src/fastqcomments.c

@@ -45,7 +45,7 @@ void destroy_read_meta(read_meta meta) {
 read_meta parse_read_meta(kstring_t comment) {
     read_meta meta = create_read_meta(&comment);
 
-    char *pch, *key, *value, *p1, *p2;
+    char *pch=NULL, *key=NULL, *value=NULL, *p1=NULL, *p2=NULL;
     pch = strtok_r(meta->comment, " ", &p1);
     while (pch != NULL) {
         // split words on `=`

src/version.h

@@ -1,2 +1,2 @@
 
-const char *argp_program_version = "0.14.0";
+const char *argp_program_version = "0.14.1";