- Rename several debug functions, modify function ProcessMisAlignInfo.
- Try to align one of end if alignment of two ends is not close to each other (in function FindSNPsFromReads).
- Ouput more info of SNP calls.
Update TODO for next improvement.
Check if alignment of two ends have:
    + Chromosome distances of seeds of two ends are small (default < 1000).
    + Distances(read, ref) are small (default <= 4). Taking into account both original and reverse complement of reads. Accepting the alignment with smallest distance.
    + Matches are in reverse strands (for Illumnia reads).
Rename several functions/variables, clean code.
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- Dismiss seeds with length less than a given value (align.go, share.go)
- Re-organize and clean code (callsnp.go, debug.go)
Clean code
Change Max_match from 32 to 16.
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- Do alignment if there is only one proper paired-seed.
- Check minimum seed length when finding seeds.
- Calculate distance threshold and number of iterations of randomization in a better way.
- Make minimum seed length and maximum seed number as input parameters.
- Print more debug info, rename several variables, clean code.
Check for maximum number of paired-seeds.