debian/changelog

-kraken (1.1-1~bpo8+1) jessie-backports-sloppy; urgency=medium
+kraken (1.1-2~bpo8+1) jessie-backports-sloppy; urgency=medium
 
   * Rebuild for jessie-backports-sloppy.
   * Revert to debhelper 10 (latest version in Jessie)
 
- -- Andreas Tille <tille@debian.org>  Tue, 06 Feb 2018 14:44:02 +0100
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 11:00:42 +0100
+
+kraken (1.1-2) unstable; urgency=medium
+
+  * Slighly more robust method to obtain taxid of fasta files to at least
+    enable reading the provided data examples of autopkgtest
+    Closes: #889623
+
+ -- Andreas Tille <tille@debian.org>  Wed, 07 Feb 2018 13:59:49 +0100
 
 kraken (1.1-1) unstable; urgency=medium
 

debian/patches/fix_reading_fasta.patch

+Description: Slighly more robust method to obtain taxid of fasta files to at
+  least enable reading the provided data examples of autopkgtest
+Bug-Debian: https://bugs.debian.org/889623
+Forwarded: https://github.com/DerrickWood/kraken/issues/111
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 07 Feb 2018 13:41:39 +0100
+
+--- a/scripts/scan_fasta_file.pl
++++ b/scripts/scan_fasta_file.pl
+@@ -32,6 +32,8 @@ while (<>) {
+   # while (/.../g) needed because non-redundant DBs sometimes have multiple
+   #   sequence IDs in the header; extra sequence IDs are prefixed by
+   #   '\x01' characters (if downloaded in FASTA format from NCBI FTP directly).
++  s/^>gi\|/>/;
++  s/\| .*//;
+   while (/(?:^>|\x01)(\S+)/g) {
+     my $seqid = $1;
+     my $taxid = krakenlib::check_seqid($seqid);

debian/patches/series

 use_jellyfish1.patch
 kraken_tmp_dir.patch
+fix_reading_fasta.patch