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I am trying to write an own special-purpose aligner for read alignment or realignment. I need some help.
Say that I have found a particular coordinate for one read of a read-pair. The mate of this read will be located within a distance of, say, +/- 500 nt. Can I rewrite an existing aligner for this purpose, i.e. find candidate locations in the neighborhood of a coordinate? I prefer C++ to C, so maybe that Bowtie 2 would be easier to wrap than BWA.
I also need an external library for fastq.gz files (FASTQ compressed with gzip). I was thinking that Boost Iostreams library would be useful. Is that good, or is there any better approach?
Say that I have found a particular coordinate for one read of a read-pair. The mate of this read will be located within a distance of, say, +/- 500 nt. Can I rewrite an existing aligner for this purpose, i.e. find candidate locations in the neighborhood of a coordinate? I prefer C++ to C, so maybe that Bowtie 2 would be easier to wrap than BWA.
I also need an external library for fastq.gz files (FASTQ compressed with gzip). I was thinking that Boost Iostreams library would be useful. Is that good, or is there any better approach?
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