A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB
to re-enable converting warnings to errors, un-comment HTS_PROG_CC_WERROR(bambi_late_cflags) in configure.ac
autoreconf -i
configure --prefix=<place to install> --with-htslib=<directory containing lib and include directory with htslib release>
eg: configure --prefix=/usr/local/bambi --with-htslib=/usr/local/htslib/1.3
or: configure --prefix=$HOME/programs --with-htslib=$CONDA_PREFIX
if conda is activated and contains htslib, pkg-config plus compilers
simply: configure --prefix=$HOME/programs
make or make -j <threads>
make check (to run tests)
make install
bambi <command> [options]
| command | description |
|---|---|
| decode | decode a multiplexed SAM/BAM/CRAM file by read groups |
| i2b | converts illumina files to SAM/BAM/CRAM files |
| select | select reads by alignment |
| chrsplit | split reads by chromosome |
| read2tags | convert reads into tags |
| spatial_filter | spatial filtering |
| seqchksum | calculate checksums for a bam file |
| adapters | find and remove adapters |
| update | update a BAM/SAM/CRAM file by RG tag |
| tag2qname | prefix qnames of a BAM/SAM/CRAM file by tag value |
| substitution_analysis | produce a substitution analysis table |