Convert samtools coverage postions to 1-based indexing instead of 0-based

[jennahamlin]

The below line needs each gene to be 1-based indexed like proA, instead of 0-based indexed for calculating coverage because samtools coverage is 1-based.

el_gato/el_gato/el_gato.py

Line 1189 in f6f17a6

coverage_command = f"samtools coverage -r flaA:351-531 {outdir}/reads_vs_all_ref_filt_sorted.bam | cut -f 1,4,5,6,7,8,9; samtools coverage -r pilE:351-682 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r asd:351-822 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r mip:350-750 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r mompS:367-717 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r proA:350-754 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuA:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuAh:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuA_207:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuA_211:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuA_212:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9; samtools coverage -r neuA_215:350-702 {outdir}/reads_vs_all_ref_filt_sorted.bam | tail -1 | cut -f 1,4,5,6,7,8,9"

These positions to calculate coverage for each gene should match the positions in the REF_POSITIONS dictionary as seen starting on Line 38, seen below:

el_gato/el_gato/el_gato.py

Line 38 in f6f17a6

REF_POSITIONS = {