Merge pull request #118 from dpryan79/fix117

Fix #117, bump version to 0.5.3

Author: dpryan79

CHANGELOG.md

@@ -1,3 +1,7 @@
+Version 0.5.3:
+
+   * Fixed an issue with the `perRead` subcommand, wherein the requireFlags option didn't fully work (a read would pass if it had at least one of the required flags set, rather than all of them). (issue #117)
+
 Version 0.5.2:
 
    * Rewrote how read-pair overlap handling is performed. It now uses the constructor/destructor mechanism from htslib instead of using internal htslib structures and functions. This allows supporting newer htslib versions. Currently 1.11 is the only tested and working version, due to changes in the pileup constructor interface in it. (issue #99)

Makefile

@@ -11,7 +11,7 @@ CFLAGS ?= -Wall -g -O3 -pthread
 all: MethylDackel
 
 OBJS = common.o bed.o svg.o overlaps.o extract.o MBias.o mergeContext.o perRead.o
-VERSION = 0.5.2
+VERSION = 0.5.3
 
 version.h:
 	echo '#define VERSION "$(VERSION)"' > $@

azure-pipeline.yml

@@ -41,6 +41,6 @@ jobs:
     displayName: Add conda to PATH
   - bash: sudo chown -R 501:20 /usr/local/miniconda/pkgs
     displayName: Fix permissions
-  - bash: conda create -n MethylDackel -q --yes -c conda-forge -c bioconda htslib=$(HTSLIB_VERSION) python clang clang_osx-64 clangxx cctools compiler-rt ld64 libbigwig
+  - bash: conda create -n MethylDackel -q --yes -c conda-forge -c bioconda htslib=$(HTSLIB_VERSION) python clang=11.1.0 clang-11 clang_osx-64=11.1.0 clangxx=11.1.0 cctools_osx-64 compiler-rt ld64_osx-64 libcxx make libbigwig
     displayName: Installing dependencies
   - template: .azure-pipelines/test-template.yml

perRead.c

@@ -188,7 +188,7 @@ void *perReadMetrics(void *foo) {
             if(b->core.pos < localPos) continue;
             if(b->core.pos >= localEnd) break;
             nmethyl = 0, nunmethyl = 0;
-            if(config->requireFlags && (config->requireFlags & b->core.flag) == 0) continue;
+            if(config->requireFlags && (config->requireFlags & b->core.flag) != config->requireFlags) continue;
             if(config->ignoreFlags && (config->ignoreFlags & b->core.flag) != 0) continue;
             if(b->core.qual < config->minMapq) continue;
             processRead(config, b, seq, localPos2, seqlen, &nmethyl, &nunmethyl);