#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

my $argc = scalar(@ARGV);

if ($argc != 1) {
  printf STDERR "usage: gapDescription.pl <buildDirectory>\n";
  printf STDERR "where <buildDirectory> is where the assembly hub is under construction.\n";
  exit 255;
}

my $wrkDir = shift;

if ( ! -d $wrkDir ) {
  printf STDERR "ERROR: can not find work directory:\n\t'%s'\n", $wrkDir;
  exit 255;
}

chdir $wrkDir;
# print STDERR `ls`;
my $accAsm = basename($wrkDir);
exit 0 if ( ! -s "bbi/${accAsm}.gap.ncbi.bb" );
my $groupName = $wrkDir;
my $asmType = "genbank";
$asmType = "refseq" if ( $groupName =~ m#/refseq/#);
$groupName =~ s#.*/$asmType/##;
$groupName =~ s#/.*##;
my $selfUrl = "${groupName}/${accAsm}";

# printf STDERR "%s\n", $accAsm;
my $htmlFile="${accAsm}.gap.html";
open (FH, ">$htmlFile") or die "can not write to $htmlFile";

my $em = "<em>";
my $noEm = "</em>";
my $assemblyDate = `grep -v "^#" $accAsm.names.tab | cut -f9`;
chomp $assemblyDate;
my $ncbiAssemblyId = `grep -v "^#" $accAsm.names.tab | cut -f10`;
chomp $ncbiAssemblyId;
my $agpFiles = `ls ${accAsm}.*.agp.ncbi.gz | xargs echo`;
chomp $agpFiles;
my $organism = `grep -v "^#" $accAsm.names.tab | cut -f5`;
chomp $organism;


print FH <<_EOF_
<h2>Description</h2>
<p>
This track shows the gaps in the $assemblyDate $em${organism}$noEm/$accAsm genome assembly.
</p>
<p>
Genome assembly procedures are covered in the NCBI
<a href="https://www.ncbi.nlm.nih.gov/assembly/basics/"
target=_blank>assembly documentation</a>.<BR>
NCBI also provides
<a href="https://www.ncbi.nlm.nih.gov/assembly/$ncbiAssemblyId"
target="_blank">specific information about this assembly</a>.
</p>
<p>
The definition of the gaps in this assembly is from the AGP file(s):<br>
$agpFiles<br>
in this <a href="/gbdb/hubs/$asmType/$selfUrl/" target=_blank>build directory</a><br>
The NCBI document
<a href="https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/"
target=_blank>AGP Specification</a> describes the format of the AGP file.
</p>
<p>
Gaps are represented as black boxes in this track.
If the relative order and orientation of the contigs on either side
of the gap is supported by read pair data, 
it is a <em>bridged</em> gap and a white line is drawn 
through the black box representing the gap. 
</p>
<p>
Return to UCSC naming <a href="/gbdb/hubs/$asmType/$groupName/${groupName}.html">$groupName</a> assembly hub index.<br>
Return to NCBI naming <a href="/gbdb/hubs/$asmType/$groupName/${groupName}.ncbi.html">$groupName</a> assembly hub index.
</p>
_EOF_
   ;

close (FH);