overlapping regions may skew alignment distribution

[cschu]

This is one of the "long gene" misannotations, which causes two regions to overlap. 1overN treats alignments to these overlapping regions as individual alignments (-> may skew count).

grep ST-K00119:83:HH22HBBXX:1:1205:6066:44359 small_test.txt 111015.SAMN04435863.CP014228 1701401 1701448 ST-K00119:83:HH22HBBXX:1:1205:6066:44359/2 0 + 1701401 1701448 0,0,0 1 47, 0, 111015.SAMN04435863.CP014228 refseq eggnog 1698783 1702742 . + . ID=111015.SAMN04435863.AXF14_07150;eggNOG_OGs=4D4KH@85005,2GKWF@201174,COG0086@2,COG0086@1;GOs=GO:0005575,GO:0008150,GO:0030312,GO:0044424,GO:0016020,GO:0044464,GO:0071944,GO:0061695,GO:1902494,GO:0005623,GO:0032991,GO:0030880,GO:0000428,GO:0040007,GO:0005618,GO:1990234,GO:0005622,GO:0005886;EC=2.7.7.6;KEGG_ko=ko:K03046;KEGG_Pathway=ko00240,map00240,ko03020,ko00230,map01100,map00230,map03020,ko01100;KEGG_Module=M00183;KEGG_Reaction=R00441,R00443,R00442,R00435;KEGG_rclass=RC02795;BRITE=ko01000,ko00000,br01611,ko03021,ko00002,ko00001,ko03400;COG_Functional_cat.=K 47 111015.SAMN04435863.CP014228 1701401 1701448 ST-K00119:83:HH22HBBXX:1:1205:6066:44359/2 0 + 1701401 1701448 0,0,0 1 47, 0, 111015.SAMN04435863.CP014228 refseq eggnog 1 3051613 . + . ID=111015.SAMN04435863.AXF14_00005;eggNOG_OGs=COG3547@1,COG3547@2,2HASG@201174;COG_Functional_cat.=L 47