Add --cycle parameter to limit read balancing iterations

v0.0.5

Add --cycle parameter to set max number for read balancing iterations

Bug fix

When we are looking for the start and end intervals
for the specific read, we iterate over our interval
map using iterator that should be restored to its
original value in following cases:

1. we failed to find start or end interval
2. we processed sliced read
   If not restored, we miss some reads due to the "jump"
   in coordinates of our annotation

Paired-end bug fix

Changes:

Excluded chromosomes should not influence
on mapped reads number. So when BAM statistics
is calculated the results are the following:

1. Total = all reads, includeing excluded chrms
2. Excluded = reads from excluded chrms
3. Aligned = Total - Excluded - NotAligned
4. NotAligned are all the reads which satisfy one
   of the criterias:
   • not mapped (0x4)
   • not primary alignment (0x100)
   • PCR or optical duplicate (0x400)
   • is paired (0x1), but is not proper pair (0x2)
   • is paired (0x1), but mate is unmapped (0x8)
     We don't need to check if paired-end reads have
     correct alignment or if they are on opposite strands
     etc, because proper pair (0x2) flag set by aligner
     is enough to make the conclusion that everything
     ok with that read (tested with STAR).

Refactore:

• excluded chromosomes are completely skipped at the
  beginning of the program. We don't load them at all

Add cutoff and exclude chromosome features

Rename arguments:

• gtf -> annotation
• threadNumber -> threads

Add arguments:

• threshold
• cutoff
• exclude

Initial release

Remove exact boost version

Causes problems on Ubuntu 16.04