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bamcc\n\n## Description\n\nA set of sequence alignments (represented as a BAM/SAM/CRAM file) defines\na bipartite graph in which the nodes are reference and template sequences\nand the edges are alignments between a template and a reference.\n\nbamcc splits this graph into connected components and reports the mapping from\nreference sequences to their components.\n\nThis is useful e.g. when analyzing multireads in an RNA-Seq experiment,\nwhere connected components can be analyzed independently.\n\n## Usage\n\n```\nbamcc input.bam output.tsv\n```\n\nThe `output.tsv` file will look like this:\n\n```\nseqid  seqname      component\n0      FBtr0005088  0\n1      FBtr0006151  1\n2      FBtr0070000  2\n3      FBtr0070002  0\n4      FBtr0070003  2\n5      FBtr0070006  3\n```\n\nwhere:\n\n1. `seqid` is the 0-based number of the reference sequence.\n    Sequence numbers are defined by the input file and are stable.\n2.  `seqname` is the reference sequence name.\n3.  `component` is the 0-based component number to which the reference has been\n    assigned.\n\nTo extract, say, the 17th component into a separate bam file, run\n\n```\nsamtools view -bh -o example.17.bam example.sorted.bam \\\n  $(awk 'BEGIN{ORS=\" \"} NR\u003e1 \u0026\u0026 $3==17 {print $2}' rsem_orig.tsv)\n```\n\n## Building\n\n### Dependencies\n\n* A C++-14 compiler\n* [htslib](http://www.htslib.org/)\n* [Boost](http://www.boost.org/)\n\n### Compilation\n\n```\nCXXFLAGS=-O2 make\n```\n\nThis will create an executable `bamcc` in the current directory.\n\n## Testing\n\nFirst, run `make`.\n\nThen, run `./test`.\nThis will update all files `test_files/example*.tsv`.\nFailures may appear either as messages from `bamcc` or differences in output\nfiles reported by `git diff`.\n\n## Security\n\nDo not run this program on untrusted or potentially malformed input files.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funkindpartition%2Fbamcc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funkindpartition%2Fbamcc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funkindpartition%2Fbamcc/lists"}