Merge branch 'dev'

ChangeLog.md

@@ -1,3 +1,14 @@
+### 0.2.0 / 2015-01-30
+Bug Fixes:
+
+* Fixed "option --num-cpu-threads not recognized"
+
+Enhancements:
+
+* `--mem-flag` option for memory control
+* `--continue` option to resume an interrupted run
+* support mixed fasta/fastq input via `kseq.h`
+
 ### 0.1.4 / 2015-01-20
 Bug Fixes:
 
@@ -7,7 +18,7 @@ Bug Fixes:
 
 Enhancements:
 
-* MAC OS X support (Thank [Laurent Gautier](https://github.com/lgautier))
+* MAC OS X support
 * Minor improvement to reduce memory usage of the SdBG builder
 
 Bug Fixes:
@@ -18,7 +29,7 @@ Bug Fixes:
 
 Enhancements:
 
-* Update Makefile and python wrapper to improve compatibility (Thank [C. Titus Brown](https://github.com/ctb) and [Ben J Woodcroft](https://github.com/wwood))
+* Update Makefile and python wrapper to improve compatibility
 * Output exit code when subprogram exit abnormally
 * Improve memory usage of the subprogram `assembler`
 * Fix the issue of minor stat differences caused by loops

README.md

@@ -1,7 +1,7 @@
 MEGAHIT
 =========
 
-MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct *de Bruijn* graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. It automatically adjusts itself to use all/moderate available memory (specified by `-m` and `--mem-flag`) to build succinct *de Bruijn* graphs. Both CPU-only and GPU-accelerated version of MEGAHIT are provided. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory).
+MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct *de Bruijn* graph (SdBG) to achieve low memory assembly. The graph construction algorithm can self-adjust to use all available or moderate memory, and can be accelerated if a CUDA-enable GPU is provided. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory).
 
 [![Build Status](https://travis-ci.org/voutcn/megahit.svg)](https://travis-ci.org/voutcn/megahit)
 [![Build Status](https://drone.io/github.com/voutcn/megahit/status.png)](https://drone.io/github.com/voutcn/megahit/latest)
@@ -10,7 +10,7 @@ Getting Started
 ----------------
 
 ### Dependency
-MEGAHIT is suitable for 64-bit Linux and MAC OS X. It requires [zlib](http://www.zlib.net/), python 2.6 or greater and G++ 4.4 or greater (with `-std=c++0x` and [OpenMP](http://openmp.org) support). The GPU version of MEGAHIT further requires [CUDA](https://developer.nvidia.com/cuda-toolkit) 5.5 or greater.
+MEGAHIT is suitable for 64-bit Linux and MAC OS X. It requires [zlib](http://www.zlib.net/), python 2.6 or greater and G++ 4.4 or greater (with `-std=c++0x` and [OpenMP](http://openmp.org) support). The GPU version further requires [CUDA](https://developer.nvidia.com/cuda-toolkit) 5.5 or greater.
 
 ### Compiling from Source Codes
 ```
@@ -31,41 +31,24 @@ If MEGAHIT is successfully compiled, it can be run by the following command:
 User can also run `./megahit -h` for the usage message.
 
 ### Using GPU Version
-To use the GPU version, run `make use_gpu=1` to compile MEGAHIT, and run MEGAHIT without `--cpu-only` option. At this stage, the GPU version only supports Linux.
+To use the GPU version, run `make use_gpu=1` to compile MEGAHIT, and run MEGAHIT without `--cpu-only` option. GPU version has only been tested in Linux.
 
 
-Memory Control
+Memory Setting
 ----------------
-We recommend to set `-m` as large as possible. In general, 90% of the free memory is recommended. This parameter is used to control the maximum memory that can be used for the SdBG construction. It is required to prevent the program from using swap space.
+Users are requried to set a memory parameter `-m` for MEGAHIT. This parameter specifies the maximum memory that can be used by the SdBG constrution conponent of MEGAHIT. `--mem-flag` is another option for memory control.
+
+### Quick recommendation
+Set the `-m` parameter to be 90-95% of the available memory and leave the `--mem-flag` default. For example if your machine have 64G available memory, a proper setting is `-m 60e9`.
+
+### Detail explanation 
+Please refer to [this wiki page](https://github.com/voutcn/megahit/wiki/MEGAHIT-Memory-setting).
 
-Since v0.2.0, it is not necessary for the SdBG builder to use up all the memory specificed by `-m`. The option `--mem-flag` specifies the ways to utilize memory: `--mem-flag 0` to use minimum memory, `--mem-flag 1` moderate memory and `--mem-flag 2` all memory.
 
 Input Files
 --------------
 
-MEGAHIT accepts one fasta or fastq file as input. The input file can be gzip'ed. Alternatively, you can use the option `--input-cmd` to input reads from multiple files. Following the `--input-cmd` should be a command that outputs all reads to `STDOUT` in fasta or fastq format. A mix of fasta and fastq is also supported. Pair-end information is not used by MEGAHIT currently. Therefore pair-end files can be input to MEGAHIT as multiple single-end files. Some examples are shown below.
-
-###Correct Examples
-* Input from one gzip'ed fastq file named *reads.fastq.gz*:
-```
--r reads.fastq.gz
-```
-* Input from two fasta files *sample_1.fa* and *sample_2.fa*:
-```
---input-cmd "cat sample_[12].fa"
-```
-* Input from all gzip'ed fastq files in current directory:
-```
---input-cmd "zcat *.fastq.gz"
-```
-* Assume that fastq-dump is installed, input from a sra file *xxx.sra*:
-```
---input-cmd "fastq-dump -Z --fasta xxx.sra"
-```
-* Mixed fastq and fasta:
-```
---input-cmd "cat 1.fa 2.fq"
-```
+MEGAHIT accepts one fasta or fastq file as input. The input file can be gzip'ed. Alternatively, you can use the option `--input-cmd` to input reads from multiple files. Following the `--input-cmd` should be a command that outputs all reads to `STDOUT` in fasta or fastq format. A mix of fasta and fastq is also supported from version 0.2.0. Currently pair-end information is not used by MEGAHIT. Therefore pair-end files can be input to MEGAHIT as multiple single-end files. Some examples are shown on [this wiki page](https://github.com/voutcn/megahit/wiki/Input-examples).
 
 Options
 ------------------------
@@ -75,11 +58,19 @@ MEGAHIT uses multiple *k*-mer strategy. Minimum *k*, maximum *k* and the step fo
 For ultra complex metagenomics data such as soil, a larger *k<sub>min</sub>*, say 27, is recommended to reduce the complexity of the *de Bruijn* graph. Quality trimming is also recommended.
 
 ###Filtering (*k<sub>min</sub>*+1)-mer
-(*k<sub>min</sub>*+1)-mer with multiplicity lower than *d* (default 2, specified by `--min-count` option) will be discarded. You should be cautious to set *d* less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2.
+(*k<sub>min</sub>*+1)-mer with multiplicity lower than *d* (default 2, specified by `--min-count` option) will be discarded. You should be cautious to set *d* less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assembly, please change this value according to the sequencing depth.
 
 ###Mercy *k*-mer
 This is specially designed for metagenomics assembly to recover low coverage sequence. You can disable it with `--no-mercy` option.
 
+Issue Report
+-----------------------
+If you have any questions or suggestions, please [report an issus](https://github.com/voutcn/megahit/issues) on Github.
+
+Cite MEGAHIT
+-----------------------
+* Li, D., *et al*. (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. *Bioinformatics*, doi: 10.1093/bioinformatics/btv033 [PMID: [25609793](http://www.ncbi.nlm.nih.gov/pubmed/25609793)].
+
 License
 -----------------------
 ```

atomic_bit_vector.h

@@ -24,12 +24,13 @@
 #include <assert.h>
 #include <stdlib.h>
 #include <memory.h>
+#include <stdint.h>
 #include <algorithm>
 #include "mem_file_checker-inl.h"
 
 class AtomicBitVector {
 public:
-    typedef unsigned long long word_t;
+    typedef uint8_t word_t;
 
     AtomicBitVector(size_t size = 0): size_(size) {
         num_words_ = ((size + kBitsPerWord - 1) / kBitsPerWord);