Empty output for the test case

[geocarvalho]

Hi, thank you for making the project open-source! I was trying to run the test case but looks like it is failing the new version. The only change I made was the grep -P to grep -E in the main script.

bash AutoMap_v1.2.sh --vcf Test/TestSample.vcf --out testing/ --genome hg19
# bcftools higher or equal to v1.9
# bedtools higher or equal to v2.24.0
# perl higher or equal to v5.22.0
# R higher or equal to v3.2.0
## Parameters used by default:
 -> No use of --DP option, value set as default: 8
 -> No use of --binomial option, value set as default: 0.000001
 -> No use of --percaltlow option, value set as default: 0.25
 -> No use of --percalthigh option, value set as default: 0.75
 -> No use of --window option, value set as default: 7
 -> No use of --windowthres option, value set as default: 5
 -> No use of --minsize option, value set as default: 1
 -> No use of --minvar option, value set as default: 25
 -> No use of --minperc option, value set as default: 88
 -> No use of --maxgap option, value set as default: 10
 -> chrX will NOT be included in the analysis and in the graphics.
 -> Homozygosity regions will be extended to nearest variant with maximum of 1 Mb.
AutoMap_v1.2.sh: line 326: [: : integer expression expected

1) Parsing of VCF file and variant filtering
 *   111569 variants before filtering
 *    80260 variants after filtering

2) Detection of ROHs with sliding window, trimming and extension
 * Treatment of the data
 * Printing of the homozygous regions

3) Filtering of regions found and output to text file
 *        0 regions before filtering
 *        0 regions after filtering with 0 Mb in total

[mquinodo]

Hi, Thank you for using AutoMap. I tried the script after changing all "grep -P" to "grep -E" and it worked normally. Is there a specific reason why you changed the grep command?

Best, Mathieu