Adjust also target ranges and make valid outputs

[AndreaGuarracino]

With this PR, now we:

• also adjust target ranges (not only query ranges)
• emit valid BEDPE and PAF outputs
• fix a few bugs.
• have a -c/--check-intervals flag to check if projected intervals are valid

[AndreaGuarracino]

Added -c/--check-intervals flag to check that the projected intervals are valid with respect to the CIGAR string:

-c, --check-intervals              Check the projected intervals, reporting the wrong ones (slow, useful for debugging)

Example (with fake errors):

impg -p scerevisiae7.s5k.p90.n1.c20k.aln.paf  -b scerevisiae.busco-genes.single.bed -c
  Query length mismatch: expected 14716 from the query range [343848-358564), got 14715 from the CIGAR string; SK1#1#chrXII	1035507	343848	358564	+	SK1#1#chrVI	298678	334149	348864	14715=
  Query length mismatch: expected 14716 from the query range [336487-351203), got 14715 from the CIGAR string; UWOPS034614#1#chrXII	1035507	336487	351203	+	SK1#1#chrVI	298678	334149	348864	72=1X569=1X41=1X86=1...
  Query length mismatch: expected 14716 from the query range [344179-358895), got 14715 from the CIGAR string; YPS128#1#chrXII	1035507	344179	358895	+	SK1#1#chrVI	298678	334149	348864	642=1X128=1X1=1X116=...
  Query length mismatch: expected 14716 from the query range [332043-346759), got 14715 from the CIGAR string; DBVPG6765#1#chrXII	1035507	332043	346759	+	SK1#1#chrVI	298678	334149	348864	129=1X446=1X194=1X1=...
  Query length mismatch: expected 14716 from the query range [349047-363763), got 14715 from the CIGAR string; S288C#1#chrXII	1035507	349047	363763	+	SK1#1#chrVI	298678	334149	348864	129=1X446=1X194=1X1=...
  Query length mismatch: expected 14695 from the query range [348060-362755), got 14694 from the CIGAR string; Y12#1#chrXII	1035507	348060	362755	+	SK1#1#chrVI	298678	334149	348864	642=1X128=1X1=1X116=...