Andreas Tille pushed to branch debian/jessie-backports-sloppy at Debian Med / kraken
Commits: 7aadb755 by Andreas Tille at 2018-02-07T12:44:48Z Slighly more robust method to obtain taxid of fasta files to at least enable reading the provided data examples of autopkgtest - - - - - d4d320a7 by Andreas Tille at 2018-02-07T12:59:23Z Forwarded issue upstream - - - - - 5b70f5b5 by Andreas Tille at 2018-02-07T13:06:36Z Upload to unstable - - - - - cfa81f03 by Andreas Tille at 2018-02-07T13:18:13Z Merge branch 'master' into debian/jessie-backports-sloppy - - - - - 5619acd2 by Andreas Tille at 2018-02-12T10:01:03Z Upload to jessie-sloppy - - - - - 3 changed files: - debian/changelog - + debian/patches/fix_reading_fasta.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,9 +1,17 @@ -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 <[email protected]> Tue, 06 Feb 2018 14:44:02 +0100 + -- Andreas Tille <[email protected]> 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 <[email protected]> Wed, 07 Feb 2018 13:59:49 +0100 kraken (1.1-1) unstable; urgency=medium ===================================== debian/patches/fix_reading_fasta.patch ===================================== @@ -0,0 +1,18 @@ +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 <[email protected]> +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 ===================================== @@ -1,2 +1,3 @@ use_jellyfish1.patch kraken_tmp_dir.patch +fix_reading_fasta.patch View it on GitLab: https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd -- View it on GitLab: https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd You're receiving this email because of your account on salsa.debian.org.
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