Merge branch 'dev'

README-alt.md

@@ -2,7 +2,7 @@
 
 ```sh
 # Download the bwa-0.7.11 binary package (download link may change)
-wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit-0.7.11_x64-linux.tar.bz2/download \
+wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
   | gzip -dc | tar xf -
 # Generate the GRCh38+ALT+decoy+HLA and create the BWA index
 bwa.kit/run-gen-ref hs38d6   # download GRCh38 and write hs38d6.fa
@@ -13,7 +13,8 @@ bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh  # skip "|sh" to show
 
 This generates `out.aln.bam` as the final alignment, `out.hla.top` for best HLA
 genotypes on each gene and `out.hla.all` for other possible HLA genotypes.
-Please check out [bwa/bwakit/README.md][kithelp] for details.
+Please check out [bwa/bwakit/README.md][kithelp] for details. If the download
+link above does not work, please acquire the binary package [here][res].
 
 ## Background
 
@@ -161,7 +162,7 @@ can even get rid of ALT contigs for good.
 
 
 
-[res]: https://sourceforge.net/projects/bio-bwa/files/
+[res]: https://sourceforge.net/projects/bio-bwa/files/bwakit
 [sb]: https://github.com/GregoryFaust/samblaster
 [grc]: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
 [novel]: https://gist.github.com/lh3/9935148b71f04ba1a8cc