[BUG] Wrong coordinates in results

[fmalmeida]

Describe the bug Hi, First thanks for the nice work on this tool. I have been using this tool in a pipeline of mine and it has been working awesomely.

Recently I tried using it with some vibrio genomes, and it has been showing problems with the annotation of integrons that happen in the very start of the sequences.

If many fails because it has sometimes generated results at the very first base and writing it as 0-index for example. And in some other, it has generated wrong negative start positions as below:

13      Integron_Finder integron        69515   74987   .       +       1       ID=integron_01;integron_type=complete
24      Integron_Finder integron        25      12675   .       +       1       ID=integron_01;integron_type=CALIN
25      Integron_Finder integron        19      9958    .       +       1       ID=integron_01;integron_type=CALIN
27      Integron_Finder integron        6936    9536    .       +       1       ID=integron_01;integron_type=complete
31      Integron_Finder integron        478     4564    .       +       1       ID=integron_01;integron_type=CALIN
32      Integron_Finder integron        66      4604    .       +       1       ID=integron_01;integron_type=CALIN
33      Integron_Finder integron        117     4047    .       +       1       ID=integron_01;integron_type=CALIN
37      Integron_Finder integron        -2      3108    .       +       1       ID=integron_01;integron_type=CALIN
38      Integron_Finder integron        2       2804    .       +       1       ID=integron_01;integron_type=CALIN
44      Integron_Finder integron        70      1709    .       +       1       ID=integron_01;integron_type=CALIN
46      Integron_Finder integron        -17     1603    .       +       1       ID=integron_01;integron_type=CALIN

I am thus, sharing the gbk files that were generated by integron_finder itself during analysis so that you can see the generated results, while at the same time having the contig sequence for reproducing it.

gbk_37_and_46.zip

To Reproduce

integron_finder --local-max --func-annot --pdf --gbk --cpu 4 vibrio31.fna

Expected behavior

The minimum allowed starting base should be 1, not 0 nor negative.

OS:

• [X] Linux
• [ ] Windows
• [ ] Mac

Integron_Finder Version:

version 2.0.1