Fixing errors with gen_infernalHits.pl, wherein all the hit coordinates were wrong in chromosome space when converted from exon-intron boundary space.

Author: biocoder

NGS-Utils/README.pod

@@ -42,7 +42,7 @@ Run the B<I<identification stage>> of the pipeline through command-line options
 
 =head1 CITATION
 
-B<Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer Progression Reveals a Global Decrease in H3K4me3 Activity> Karen Triff; Mathew W McLean; Kranti Kranti; Jiahui Pang; Evelyn Callaway; Beiyan Zhou; Ivan Ivanov; Robert S. Chapkin B<I<Molecular Basis of Disease 2017>>
+B<Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer Progression Reveals a Global Decrease in H3K4me3 Activity> Karen Triff; Mathew W McLean; Kranti Konganti; Jiahui Pang; Evelyn Callaway; Beiyan Zhou; Ivan Ivanov; Robert S. Chapkin B<I<Molecular Basis of Disease 2017>>
 
 =head1 INSTALLATION
 
@@ -837,6 +837,6 @@ This program is distributed under the Artistic License 2.0.
 
 =head1 DATE
 
-Mar-22-2018
+Oct-04-2019
 
 =cut

NGS-Utils/blast2gff.pl

@@ -116,7 +116,8 @@
                                                                -seq_name => $hit->name,
                                                                -tag => {query_id => $query_name,
 							                hit_ident => $percent_identity,
-							                hsp_match_len => $hsp->length('total')},
+							                hsp_match_len => $hsp->length('total'),
+									query_cov => $query_coverage},
                                                                -score => $hsp->score,
                                                                -start => $corresponding_chr_start,
                                                                -end => $corresponding_chr_end,