diff --git a/CHANGELOG.md b/CHANGELOG.md index 48b3dac..f794d87 100644 --- 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 index 97c14f1..233e95e 100644 --- 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 index abb8870..1819560 100644 --- a/src/definitions.h +++ b/src/definitions.h @@ -18,13 +18,13 @@ /* contact: Dinghua Li */ -#ifndef MEGAHIT_DEFINITIONS_H__ -#define MEGAHIT_DEFINITIONS_H__ +#ifndef MEGAHIT_DEFINITIONS_H +#define MEGAHIT_DEFINITIONS_H #include #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 GenericKmer; -#endif // MEGAHIT_DEFINITIONS_H__ +#endif // MEGAHIT_DEFINITIONS_H diff --git a/src/localasm/local_assembler.h b/src/localasm/local_assembler.h index f707a0f..ebdf1ea 100644 --- a/src/localasm/local_assembler.h +++ b/src/localasm/local_assembler.h @@ -18,8 +18,8 @@ /* contact: Dinghua Li */ -#ifndef LOCAL_ASSEMBLER_H__ -#define LOCAL_ASSEMBLER_H__ +#ifndef LOCAL_ASSEMBLER_H +#define LOCAL_ASSEMBLER_H #include #include diff --git a/src/sequence/io/lib_info.h b/src/sequence/io/lib_info.h index 595ec42..040b6d9 100644 --- a/src/sequence/io/lib_info.h +++ b/src/sequence/io/lib_info.h @@ -20,8 +20,8 @@ /* contact: Dinghua Li */ -#ifndef LIB_INFO_H__ -#define LIB_INFO_H__ +#ifndef LIB_INFO_H +#define LIB_INFO_H #include #include diff --git a/src/sequence/io/lib_io.h b/src/sequence/io/lib_io.h index 035f089..80fb7ea 100644 --- a/src/sequence/io/lib_io.h +++ b/src/sequence/io/lib_io.h @@ -18,8 +18,8 @@ /* contact: Dinghua Li */ -#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 #include diff --git a/src/sequence/packed_reads.h b/src/sequence/packed_reads.h index 4f2e57f..fa9965e 100644 --- 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 #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 index 10a2988..6a0c336 100644 --- 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 #include diff --git a/src/utils/utils.h b/src/utils/utils.h index 06c5ea3..1475e57 100644 --- a/src/utils/utils.h +++ b/src/utils/utils.h @@ -18,8 +18,8 @@ /* contact: Dinghua Li */ -#ifndef MEGAHIT_UTILS_H__ -#define MEGAHIT_UTILS_H__ +#ifndef MEGAHIT_UTILS_H +#define MEGAHIT_UTILS_H #include #include @@ -139,4 +139,4 @@ struct AutoMaxRssRecorder { } }; -#endif // MEGAHIT_UTILS_H__ \ No newline at end of file +#endif // MEGAHIT_UTILS_H \ No newline at end of file