Hi,

I am using TFBSTools with JASPAR2016 library to scan a pairwise alignment.

The command im using is as follows:

> sitePairSet <- searchPairBSgenome(pwm, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Oaries.UCSC.oviAri3, chr1="chr29", chr2="OAR21", min.score="80%", strand="*", chain=chain)

Error: subscript contains NAs

I have tried to omit the strand but i got the same error.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12 (Sierra)

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics 
[5] grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] BiocInstaller_1.24.0             
 [2] BSgenome.Oaries.UCSC.oviAri3_3.1 
 [3] BSgenome.Btaurus.UCSC.bosTau6_3.1
 [4] TFBSTools_1.12.0                 
 [5] BSgenome_1.42.0                  
 [6] rtracklayer_1.34.0               
 [7] Biostrings_2.42.0                
 [8] XVector_0.14.0                   
 [9] GenomicRanges_1.26.0             
[10] GenomeInfoDb_1.10.0              
[11] IRanges_2.8.0                    
[12] S4Vectors_0.12.0                 
[13] BiocGenerics_0.20.0              
[14] JASPAR2016_1.2.0                 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                
 [2] plyr_1.8.4                 
 [3] R.methodsS3_1.7.1          
 [4] R.utils_2.4.0              
 [5] bitops_1.0-6               
 [6] tools_3.3.1                
 [7] zlibbioc_1.20.0            
 [8] annotate_1.52.0            
 [9] gtable_0.2.0               
[10] RSQLite_1.0.0              
[11] tibble_1.2                 
[12] lattice_0.20-34            
[13] Matrix_1.2-7.1             
[14] DBI_0.5-1                  
[15] DirichletMultinomial_1.16.0
[16] seqLogo_1.40.0             
[17] stringr_1.1.0              
[18] gtools_3.5.0               
[19] caTools_1.17.1             
[20] grid_3.3.1                 
[21] Biobase_2.34.0             
[22] poweRlaw_0.60.3            
[23] AnnotationDbi_1.36.0       
[24] XML_3.98-1.4               
[25] BiocParallel_1.8.0         
[26] VGAM_1.0-2                 
[27] GO.db_3.4.0                
[28] readr_1.0.0                
[29] reshape2_1.4.1             
[30] ggplot2_2.1.0              
[31] CNEr_1.10.0                
[32] magrittr_1.5               
[33] splines_3.3.1              
[34] scales_0.4.0               
[35] Rsamtools_1.26.0           
[36] GenomicAlignments_1.10.0   
[37] assertthat_0.1             
[38] SummarizedExperiment_1.4.0 
[39] xtable_1.8-2               
[40] colorspace_1.2-7           
[41] TFMPvalue_0.0.6            
[42] stringi_1.1.2              
[43] munsell_0.4.3              
[44] RCurl_1.95-4.8             
[45] R.oo_1.20.0                

Thanks for the report.

This has been fixed in both release and development branches and will appear on Bioconductor soon.