Update dependency for bwcat

MANIFEST

@@ -1,3 +1,5 @@
+.travis.yml
+bin/bam2bedgraph
 bin/bam_stats.pl
 bin/bam_to_sra_sub.pl
 bin/bamToBw.pl
@@ -9,6 +11,7 @@ bin/gnos_pull.pl
 bin/monitor.pl
 bin/xam_coverage_bins.pl
 bin/xml_to_bas.pl
+c/bam2bedgraph.c
 c/bam_access.c
 c/bam_access.h
 c/bam_stats.c
@@ -27,6 +30,7 @@ c/dbg.h
 c/khash.h
 c/reheadSQ.c
 CHANGES.md
+dists/patch/Bio-BigFile_build.patch
 dists/snappy-1.1.2.tar.gz
 docs.tar.gz
 examples/gnos_pull.ini

lib/PCAP.pm

@@ -26,7 +26,7 @@ use base 'Exporter';
 use FindBin qw($Bin);
 use File::Which qw(which);
 
-our $VERSION = '3.0.1';
+our $VERSION = '3.1.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>
@@ -82,6 +82,7 @@ const my %UPGRADE_PATH => ( # all earlier versions need full upgrade
                             '2.4.0' => 'biobambam',
                             '2.5.0' => 'biobambam',
                             '3.0.0' => '',
+                            '3.1.0' => '',
                           );
 
 sub license {

setup.sh

@@ -16,7 +16,7 @@ SOURCE_JKENT_BIN="https://github.com/ENCODE-DCC/kentUtils/raw/master/bin/linux.x
 SOURCE_KENTSRC="ftp://ftp.sanger.ac.uk/pub/cancer/legacy-dependancies/jksrc.v334.zip"
 SOURCE_BIGFILE="http://www.cpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz"
 # for fast merging of per-chr BW files
-SOURCE_LIB_BW="https://github.com/dpryan79/libBigWig/archive/0.1.6.tar.gz"
+SOURCE_LIB_BW="https://github.com/dpryan79/libBigWig/archive/b36da5a06bffcc1b33c369e078b82f84625fd212.tar.gz"
 
 # for biobambam
 SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.54-release-20160802163650/biobambam2-2.0.54-release-20160802163650-x86_64-etch-linux-gnu.tar.gz"
@@ -350,4 +350,4 @@ echo "Please add the following to beginning of PERL5LIB:"
 echo "  $PERLROOT"
 echo
 
-exit 0
+exit 0