From 2261c53d2e7c99d03760ae6d4a45c85160a93ba1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= Date: Tue, 25 May 2021 17:12:35 +0200 Subject: [PATCH] Changed name to CompAIRR and version to 0.1.0 --- README.md | 18 +++++++++--------- src/Makefile | 18 +++++++++--------- src/arch.cc | 2 +- src/bloompat.cc | 2 +- src/cluster.cc | 2 +- src/{vdjsearch.cc => compairr.cc} | 2 +- src/{vdjsearch.h => compairr.h} | 6 +++--- src/db.cc | 2 +- src/hashtable.cc | 2 +- src/overlap.cc | 2 +- src/util.cc | 2 +- src/variants.cc | 2 +- src/zobrist.cc | 2 +- 13 files changed, 31 insertions(+), 31 deletions(-) rename src/{vdjsearch.cc => compairr.cc} (99%) rename src/{vdjsearch.h => compairr.h} (97%) diff --git a/README.md b/README.md index 10aa25b..40608da 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ -# vdjsearch +# CompAIRR -The command line tool `vdjsearch` can be used to compare two sets of -immune receptor repertoires. It can also be used to cluster the -sequences in a repertoire. +CompAIRR (`compairr`) is a command line tool to compare two sets of +immune receptor repertoires, or cluster the sequences in one +repertoire. ## General options @@ -107,9 +107,9 @@ input. ## Command line options ``` -vdjsearch 0.0.4 - Immune repertoire analysis +CompAIRR 0.1.0 - Compare Adaptive Immune Receptor Repertoires -Usage: vdjsearch [OPTIONS] TSVFILE1 [TSVFILE2] +Usage: compairr [OPTIONS] TSVFILE1 [TSVFILE2] Commands: -h, --help display this help and exit @@ -150,12 +150,12 @@ CASSTSHQQYF 0.07 TCRBV07-06 TCRBJ02-01 B2 We run the following command: -`vdjsearch -m -d 1 -o output.tsv seta.tsv setb.tsv` +`compairr -m -d 1 -o output.tsv seta.tsv setb.tsv` Here is the output to the console: ``` -vdjsearch 0.0.4 - Immune repertoire analysis +CompAIRR 0.1.0 - Immune repertoire analysis Command: Overlap Repertoire set 1: seta.tsv @@ -265,7 +265,7 @@ 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 24 544 336 sequences. The test was performed with -vdjsearch version 0.0.3. The timing results are shown below. +version 0.0.3 of the tool. The timing results are shown below. Distance | Indels | Threads | Time (s) | Time (mm:ss) -------: | :----: | ------: | -------: | -----------: diff --git a/src/Makefile b/src/Makefile index 0184fbb..dbe6763 100644 --- a/src/Makefile +++ b/src/Makefile @@ -17,7 +17,7 @@ # Department of Informatics, University of Oslo, # PO Box 1080 Blindern, NO-0316 Oslo, Norway -# Makefile for vdjsearch +# Makefile for CompAIRR COMMON = -g -std=c++11 EXTRAOBJ = @@ -69,24 +69,24 @@ LINKFLAGS = $(COMMON) $(LINKOPT) CXXFLAGS = $(COMMON) $(WARNINGS) -PROG = vdjsearch +PROG = compairr -OBJS = arch.o bloompat.o cluster.o db.o hashtable.o overlap.o \ - util.o variants.o vdjsearch.o zobrist.o +OBJS = arch.o bloompat.o cluster.o compairr.o db.o hashtable.o \ + overlap.o util.o variants.o zobrist.o DEPS = Makefile threads.h \ - arch.h bloompat.h cluster.h db.h hashtable.h overlap.h \ - util.h variants.h vdjsearch.h zobrist.h + arch.h bloompat.h cluster.h compairr.h db.h hashtable.h \ + overlap.h util.h variants.h zobrist.h all : $(PROG) -vdjsearch : $(OBJS) $(DEPS) +compairr : $(OBJS) $(DEPS) $(CXX) $(LINKFLAGS) -o $@ $(OBJS) $(LIBS) mkdir -p ../bin - cp -a vdjsearch ../bin + cp -a compairr ../bin clean : - rm -rf vdjsearch *.o *~ gmon.out *.gcno *.gcda *.gcov + rm -rf compairr *.o *~ gmon.out *.gcno *.gcda *.gcov .o : .cc $(DEPS) $(CXX) $(CXXFLAGS) -c -o $@ $< diff --git a/src/arch.cc b/src/arch.cc index 256aa42..2ef07bf 100644 --- a/src/arch.cc +++ b/src/arch.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" uint64_t arch_get_memused() { diff --git a/src/bloompat.cc b/src/bloompat.cc index 0cbeae6..94a8c6c 100644 --- a/src/bloompat.cc +++ b/src/bloompat.cc @@ -29,7 +29,7 @@ https://doi.org/10.1145/1498698.1594230 */ -#include "vdjsearch.h" +#include "compairr.h" void bloom_patterns_generate(struct bloom_s * b); diff --git a/src/cluster.cc b/src/cluster.cc index 3c82c71..15eba57 100644 --- a/src/cluster.cc +++ b/src/cluster.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" const unsigned int no_cluster = UINT_MAX; diff --git a/src/vdjsearch.cc b/src/compairr.cc similarity index 99% rename from src/vdjsearch.cc rename to src/compairr.cc index fd3afcf..4cb029f 100644 --- a/src/vdjsearch.cc +++ b/src/compairr.cc @@ -38,7 +38,7 @@ */ -#include "vdjsearch.h" +#include "compairr.h" /* OPTIONS */ diff --git a/src/vdjsearch.h b/src/compairr.h similarity index 97% rename from src/vdjsearch.h rename to src/compairr.h index 78ab49c..8cc175e 100644 --- a/src/vdjsearch.h +++ b/src/compairr.h @@ -95,9 +95,9 @@ static_assert(INT_MAX > 32767, "Your compiler uses very short integers."); /* constants */ -#define PROG_CMD "vdjsearch" -#define PROG_NAME "VDJsearch" -#define PROG_VERSION "0.0.5" +#define PROG_CMD "compairr" +#define PROG_NAME "CompAIRR" +#define PROG_VERSION "0.1.0" #define PROG_BRIEF "Compare Adaptive Immune Receptor Repertoires" const unsigned int MAX_THREADS = 256; diff --git a/src/db.cc b/src/db.cc index 1ba45d4..0e68e21 100644 --- a/src/db.cc +++ b/src/db.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" /* How much memory for residues and sequences should we allocate each time? */ diff --git a/src/hashtable.cc b/src/hashtable.cc index 721cb39..8c6bbfb 100644 --- a/src/hashtable.cc +++ b/src/hashtable.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" #define HASHFILLPCT 70 diff --git a/src/overlap.cc b/src/overlap.cc index 2e846fb..d047233 100644 --- a/src/overlap.cc +++ b/src/overlap.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" static struct db * d; static unsigned int set1_longestsequence = 0; diff --git a/src/util.cc b/src/util.cc index b0946c8..5b6f094 100644 --- a/src/util.cc +++ b/src/util.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" static const char * progress_prompt; static uint64_t progress_next; diff --git a/src/variants.cc b/src/variants.cc index 33d93f3..a02ebb8 100644 --- a/src/variants.cc +++ b/src/variants.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" //#define DUMP 1 #define SMART 1 diff --git a/src/zobrist.cc b/src/zobrist.cc index 5826a68..be0b18a 100644 --- a/src/zobrist.cc +++ b/src/zobrist.cc @@ -19,7 +19,7 @@ PO Box 1080 Blindern, NO-0316 Oslo, Norway */ -#include "vdjsearch.h" +#include "compairr.h" uint64_t * zobrist_tab_base = nullptr; static uint64_t * zobrist_v_base = nullptr;