release 1.2.5-beta

voutcn · Jun 29, 2019 · 20c528e · 20c528e
1 parent 24c9698
commit 20c528e
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Showing 9 changed files with 25 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+### 1.2.5-beta / 2019-06-28 PST
+-   Fixed a bug that causes higher memory usage in seq2sdbg
+-   Refactor on sequence sorters, edge I/O and contig I/O
+
 ### 1.2.4-beta / 2019-05-25 PST
 -   Fixed a few memory leaks
 -   Use std::vector to replace malloc in SDBG builders

diff --git a/README.md b/README.md
@@ -24,9 +24,9 @@ Past versions can be found at the [release](https://github.com/voutcn/megahit/re
 ### Running with Linux binaries or docker images (recommended)
 
 ``` sh
-wget https://github.com/voutcn/megahit/releases/download/v1.2.4-beta/MEGAHIT-1.2.4-beta-Linux-static.tar.gz
-tar zvxf MEGAHIT-1.2.4-beta-Linux-static.tar.gz
-cd MEGAHIT-1.2.4-beta-Linux-static/bin/
+wget https://github.com/voutcn/megahit/releases/download/v1.2.5-beta/MEGAHIT-1.2.5-beta-Linux-static.tar.gz
+tar zvxf MEGAHIT-1.2.5-beta-Linux-static.tar.gz
+cd MEGAHIT-1.2.5-beta-Linux-static/bin/
 ./megahit --test  # run on a toy dataset
 ./megahit -1 YOUR_PE_READ_1.gz -2 YOUR_PE_READ_2.fq.gz -o YOUR_OUTPUT_DIR
 ```

diff --git a/src/definitions.h b/src/definitions.h
@@ -18,13 +18,13 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
-#ifndef MEGAHIT_DEFINITIONS_H__
-#define MEGAHIT_DEFINITIONS_H__
+#ifndef MEGAHIT_DEFINITIONS_H
+#define MEGAHIT_DEFINITIONS_H
 
 #include <stdint.h>
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "v1.2.4-beta"
+#define PACKAGE_VERSION "v1.2.5-beta"
 #endif
 
 #include "sdbg/sdbg_def.h"
@@ -47,4 +47,4 @@ static const int kUint64PerIdbaKmerMaxK = (kMaxK * 2 + 16 + 63) / 64;
 #include "sequence/kmer.h"
 typedef Kmer<kUint32PerKmerMaxK, uint32_t> GenericKmer;
 
-#endif  // MEGAHIT_DEFINITIONS_H__
+#endif  // MEGAHIT_DEFINITIONS_H
diff --git a/src/localasm/local_assembler.h b/src/localasm/local_assembler.h
@@ -18,8 +18,8 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
-#ifndef LOCAL_ASSEMBLER_H__
-#define LOCAL_ASSEMBLER_H__
+#ifndef LOCAL_ASSEMBLER_H
+#define LOCAL_ASSEMBLER_H
 
 #include <stdint.h>
 #include <deque>

diff --git a/src/sequence/io/lib_info.h b/src/sequence/io/lib_info.h
@@ -20,8 +20,8 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
-#ifndef LIB_INFO_H__
-#define LIB_INFO_H__
+#ifndef LIB_INFO_H
+#define LIB_INFO_H
 
 #include <stdint.h>
 #include <string>

diff --git a/src/sequence/io/lib_io.h b/src/sequence/io/lib_io.h
@@ -18,8 +18,8 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
-#ifndef READ_LIB_FUNCTIONS_INL_H__
-#define READ_LIB_FUNCTIONS_INL_H__
+#ifndef READ_LIB_FUNCTIONS_INL_H
+#define READ_LIB_FUNCTIONS_INL_H
 
 #include <inttypes.h>
 #include <stdint.h>

diff --git a/src/sequence/packed_reads.h b/src/sequence/packed_reads.h
@@ -22,8 +22,8 @@
  * Functions for packed reads or edges (ACGT -> 0123, packed by uint32_t)
  */
 
-#ifndef PACKED_READS_H__
-#define PACKED_READS_H__
+#ifndef PACKED_READS_H
+#define PACKED_READS_H
 
 #include <algorithm>
 #include "definitions.h"
@@ -152,4 +152,4 @@ inline void CopySubstringRC(uint32_t *dest, const uint32_t *src_read, unsigned o
   }
 }
 
-#endif  // PACKED_READS_H__
+#endif  // PACKED_READS_H
diff --git a/src/utils/histgram.h b/src/utils/histgram.h
@@ -7,9 +7,9 @@
  * @modified by Dinghua Li
  */
 
-#ifndef __BASIC_HISTGRAM_H__
+#ifndef __BASIC_HISTGRAM_H
 
-#define __BASIC_HISTGRAM_H__
+#define __BASIC_HISTGRAM_H
 
 #include <algorithm>
 #include <cmath>

diff --git a/src/utils/utils.h b/src/utils/utils.h
@@ -18,8 +18,8 @@
 
 /* contact: Dinghua Li <dhli@cs.hku.hk> */
 
-#ifndef MEGAHIT_UTILS_H__
-#define MEGAHIT_UTILS_H__
+#ifndef MEGAHIT_UTILS_H
+#define MEGAHIT_UTILS_H
 
 #include <fcntl.h>
 #include <cstdarg>
@@ -139,4 +139,4 @@ struct AutoMaxRssRecorder {
   }
 };
 
-#endif  // MEGAHIT_UTILS_H__
+#endif  // MEGAHIT_UTILS_H