BaseVar has been fully implemented by C++. Great improvements were made in the C++ implemetation compare to the original Python version. Now, the computing speed of BaseVar is more than 20 times faster than the Python version, and requires much less memory. Generally, each thread (-t/--thread) requires only 3GB to 4GB if -B (--batch-count) option is set to 200, while the Python version need more than 20GB.
Build the source codes step-by-step.
1. Download BaseVar from github
$ git clone --recursive https://github.com/ShujiaHuang/basevar.gitWARNING: Please try several times if fail to clone the data causing by the network problem.
2. Shift to htscodecs directory and run the following commands
$ cd htslib/htscodecs
$ autoreconf -i
$ ./configure
$ make
3. Go back to the upper directory and install main htslib by running the commands below
$ cd htslib
$ autoreconf -i
$ ./configure
$ make
Note: If you hit something like the following error information when compile the htslib above, we can ignore it
and the codes should still works fine.
test/test_khash.c: In function 'write_stats_str2int':
test/test_khash.c:53:9: warning: implicit declaration of function 'kh_stats' [-Wimplicit-function-declaration]
53 | if (kh_stats(str2int, h, &empty, &deleted, &hist_size, &hist) == 0) {
| ^~~~~~~~
test/test_khash.c:53:18: error: 'str2int' undeclared (first use in this function)
53 | if (kh_stats(str2int, h, &empty, &deleted, &hist_size, &hist) == 0) {
| ^~~~~~~
test/test_khash.c:53:18: note: each undeclared identifier is reported only once for each function it appears in
make: *** [test/test_khash.o] Error 14. Go back to the upper directory and install basevar by running the commands below
For MacOS
$ cd bin/
$ g++ -O3 -fPIC ../src/main.cpp ../src/basetype.h ../src/basetype.cpp ../src/basetype_caller.cpp ../src/utils.cpp ../src/fasta.cpp ../src/bam_header.cpp ../src/bam.cpp ../src/bam_record.cpp ../src/basetype_utils.cpp ../htslib/libhts.a -I ../htslib -lz -lbz2 -lm -llzma -lpthread -lcurl -o basevar
For Linux
$ cd bin/
$ g++ -O3 -fPIC ../src/main.cpp ../src/basetype.h ../src/basetype.cpp ../src/basetype_caller.cpp ../src/utils.cpp ../src/fasta.cpp ../src/bam_header.cpp ../src/bam.cpp ../src/bam_record.cpp ../src/basetype_utils.cpp ../htslib/libhts.a -I ../htslib -lz -lbz2 -lm -llzma -lpthread -lcurl -lssl -lcrypto -o basevar
basevar basetype -R reference.fasta \
-I 00alzqq6jw.bam \
-I 09t3r9n2rg.bam \
-I 0fkpl1p55b.bam \
-I 13dg1gvsfk.bam \
-I 17phildszl.bam \
-I 1dbpgqt0dq.bam \
-I 1kyws27hoc.bam \
--pop-group=sample_group.info \
--regions=chr11:5246595-5248428,chr17:41197764-41276135 \
-B 200 -t 4 \
--output-vcf test.vcf.gz \
--output-cvg test.cvg.tsv.gzThe format of sample_group.info could be found here.
basevar basetype -R reference.fasta -L bamfile.list \
--regions=chr11:5246595-5248428,chr17:41197764-41276135 \
-B 200 -t 4 \
--output-vcf test.vcf.gz \
--output-cvg test.cvg.tsv.gz