Warnings should be less

[Konstantin Okonechnikov]

There are sometimes too many warnings when too many reads. It's better to report warning only once.

Example: WARNING: read alignment start is greater than end: 488735221 > 488735220

However, there could be hundreds of such alignments. In this case it's better just to count warning and report the last number in the end.

[Konstantin Okonechnikov]

Fixed