diff --git a/README.md b/README.md index bc975ab..441cbea 100644 --- a/README.md +++ b/README.md @@ -134,7 +134,7 @@ ignored. ## Command line options ``` -CompAIRR 0.2.0 - Compare Adaptive Immune Receptor Repertoires +CompAIRR 1.0.0 - Compare Adaptive Immune Receptor Repertoires https://github.com/uio-bmi/compairr Usage: compairr [OPTIONS] TSVFILE1 [TSVFILE2] @@ -185,7 +185,7 @@ We run the following command: Here is the output to the console: ``` -CompAIRR 0.2.0 - Immune repertoire analysis +CompAIRR 1.0.0 - Immune repertoire analysis https://github.com/uio-bmi/compairr Command: Overlap @@ -294,7 +294,7 @@ As a preliminary performance test, Cohort 2 ("Keck") of [the dataset](https://s3-us-west-2.amazonaws.com/publishedproject-supplements/emerson-2017-natgen/emerson-2017-natgen.zip) by Emerson et al. was compared to itself. It contains 120 repertoires with a total of 24 205 557 extracted sequences. The test was performed -with CompAIRR version 0.2.0. The timing results are shown below. +with CompAIRR version 1.0.0. The timing results are shown below. Distance | Indels | Threads | Time (s) | Time (mm:ss) -------: | :----: | ------: | -------: | -----------: @@ -314,7 +314,7 @@ per sequence. Since this is a comparison of a repertoire set to itself, the dataset is only read once, and the memory needed is also reduced as compared -to a situation were two different repertoire sets were compared. +to a situation were two different repertoire sets are compared. Wall time and memory usage was measured by `/usr/bin/time`. The analysis was performed on a Mac Mini M1. @@ -326,8 +326,8 @@ The code has been developed by Torbjørn Rognes based on code from Swarm where Frédéric Mahé and Lucas Czeck made important contributions. Geir Kjetil Sandve had the idea of developing a tool for rapid repertoire set comparison. Lonneke Scheffer has tested and -benchmarked the tool, and suggested new features. Milena Pavlovic has -also contributed to the project. +benchmarked the tool, and suggested new features. Milena Pavlovic and +Victor Greiff have also contributed to the project. ## Citing CompAIRR @@ -336,10 +336,9 @@ We are preparing a manuscript about CompAIRR, but it is not yet available. For the time being, please cite the following if you use CompAIRR in any published work: -* Rognes T, Scheffer L, Sandve GK (2021) -**CompAIRR: Efficient computation of similarities between adaptive -immune receptor repertoires allowing non-exact sequence matching.** -(In prep.) +* Rognes T, Scheffer L, Greiff V, Sandve GK (2021) +**CompAIRR: Efficient computation of adaptive immune receptor repertoire-similarity allowing non-exact sequence matching.** +(in prep.) ## Support diff --git a/src/Makefile b/src/Makefile index 3c4542e..d7890a0 100644 --- a/src/Makefile +++ b/src/Makefile @@ -23,8 +23,7 @@ COMMON = -g -std=c++11 EXTRAOBJ = LINKOPT = LIBS = -lpthread -WARNINGS = -Wall -Wextra \ -#-Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic +WARNINGS = -Wall -Wextra # Run "make RELEASE=1" to compile for release ifdef RELEASE @@ -84,7 +83,7 @@ compairr : $(OBJS) $(DEPS) $(CXX) $(LINKFLAGS) -o $@ $(OBJS) $(LIBS) clean : - rm -rf compairr *.o *~ gmon.out *.gcno *.gcda *.gcov + rm -f compairr *.o *~ gmon.out *.gcno *.gcda *.gcov .o : .cc $(DEPS) $(CXX) $(CXXFLAGS) -c -o $@ $< diff --git a/src/compairr.h b/src/compairr.h index 0fdaa1d..477d342 100644 --- a/src/compairr.h +++ b/src/compairr.h @@ -98,7 +98,7 @@ static_assert(INT_MAX > 32767, "Your compiler uses very short integers."); #define PROG_CMD "compairr" #define PROG_NAME "CompAIRR" -#define PROG_VERSION "0.2.0" +#define PROG_VERSION "1.0.0" #define PROG_BRIEF "Compare Adaptive Immune Receptor Repertoires" const unsigned int MAX_THREADS = 256;