fix overcounting issue for incompatible counts

[cying111]

This branch fix for two bugs that impacts quantification:

1. overcounting of incompatible reads for each gene
2. singe exon reads mis-assignment due to re-ordering of data

[codecov-commenter]

Codecov Report

Merging #401 (931c63e) into devel (42dbb39) will not change coverage. The diff coverage is 100.00%.

:exclamation: Current head 931c63e differs from pull request most recent head 171110c. Consider uploading reports for the commit 171110c to get more accurate results

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@@           Coverage Diff           @@
##            devel     #401   +/-   ##
=======================================
  Coverage   86.32%   86.32%           
=======================================
  Files          24       24           
  Lines        3226     3226           
=======================================
  Hits         2785     2785           
  Misses        441      441           

Files	Coverage Δ
R/bambu-quantify_utilityFunctions.R	94.73% <100.00%> (ø)

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