librg-utils-perl (1.0.43) unstable; urgency=low

  * librg-utils-perl.spec.in added
  * fixed warnings caused by buggy blast output

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 28 Oct 2011 22:10:33 +0200

librg-utils-perl (1.0.42) unstable; urgency=low

  * deprecated defined %hash are rewritten
  * deprecated $[ are silenced with no warnings 'deprecated';
  * Build.PL now generated from Build.PL.in

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 28 Sep 2011 15:05:36 +0200

librg-utils-perl (1.0.41) UNRELEASED; urgency=low

  * marginally better error reporting
  * debianization moved out of this package

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 30 Jun 2011 15:17:53 +0200

librg-utils-perl (1.0.40) unstable; urgency=low

  * allow digits in dbswiss table name
  * silence warnings in non-debug mode

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 27 Jun 2011 18:12:21 +0200

librg-utils-perl (1.0.39) unstable; urgency=low

  * fixed blast+ parsing compatibility issue

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 27 Jun 2011 13:20:38 +0200

librg-utils-perl (1.0.38) unstable; urgency=low

  * now parses blast+ blastpgp output

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 22 Jun 2011 12:40:00 +0200

librg-utils-perl (1.0.37) unstable; urgency=low

  * Newline in left-justified string for sprintf warnings fixed

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 21 Jun 2011 20:10:34 +0200

librg-utils-perl (1.0.36) unstable; urgency=low

  * fixed blast to saf conversion for blast 'Query: 0   ----' bug

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 20 May 2011 21:38:33 +0200

librg-utils-perl (1.0.35) stable; urgency=low

  * fixed blast2saf.pl problem triggered by very strange looking blast alignment

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 14 Apr 2011 15:59:51 +0200

librg-utils-perl (1.0.34) stable; urgency=low

  * moved runNewPSIC.pl to its own package rost-runpsic

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 12 Apr 2011 12:22:56 +0200

librg-utils-perl (1.0.33) stable; urgency=low

  * blastpgp_to_saf.pl line 15 warning cleared

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 18 Feb 2011 18:45:45 +0100

librg-utils-perl (1.0.32) stable; urgency=low

  * blast2saf.pl warning on line 216 cleared

 -- Laszlo Kajan <lkajan@rostlab.org>  Sun, 30 Jan 2011 21:14:25 +0100

librg-utils-perl (1.0.31) stable; urgency=low

  * blast2saf.pl syntax error fixed

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 28 Jan 2011 22:54:07 +0100

librg-utils-perl (1.0.30) stable; urgency=low

  * blast2saf.pl and blastpgp_to_saf.pl much cleaner logic for reading
    last record of blast results

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 28 Jan 2011 16:28:50 +0100

librg-utils-perl (1.0.29) stable; urgency=low

  * blast2saf.pl and blastpgp_to_saf.pl bugs introduced in prev version
    fixed

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 27 Jan 2011 16:26:34 +0100

librg-utils-perl (1.0.28) stable; urgency=low

  * blast2saf.pl and blastpgp_to_saf.pl are now capable of parsing a blast
    file that does not have the footer part but just ends after a record

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 27 Jan 2011 15:28:46 +0100

librg-utils-perl (1.0.27) stable; urgency=low

  * silenced safFilterRed.pl in non-verbose non-debug mode

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 26 Jan 2011 12:58:38 +0100

librg-utils-perl (1.0.26) stable; urgency=low

  * renamed dbSwiss.pl to dbSwiss, added man page

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 26 Jan 2011 10:07:31 +0100

librg-utils-perl (1.0.25) stable; urgency=low

  * added dbSwiss.pl

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 24 Jan 2011 22:30:37 +0100

librg-utils-perl (1.0.24) stable; urgency=low

  * fixed endless loop bug

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 21 Jan 2011 16:22:47 +0100

librg-utils-perl (1.0.23) stable; urgency=low

  * Added --use-blastfile cmd line argument
  * Recoded parts to make it more readable
  * Made certain blast problems (incorrect blast file) lethal
  * Disabled 'rerun blast if too big blast input file' feature
  * Added logic to read only first 300 alignments from blast file
    that satisfy the percent identity limit requirements

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 21 Jan 2011 15:35:02 +0100

librg-utils-perl (1.0.22) stable; urgency=low

  * Fixed min-seqlen = 50 issue

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 20 Jan 2011 14:19:23 +0100

librg-utils-perl (1.0.21) stable; urgency=low

  * Recommends clustalw - runNewPSIC.pl requires it

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 19 Jan 2011 17:33:01 +0100

librg-utils-perl (1.0.20) stable; urgency=low

  * psic Depends added

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 19 Jan 2011 17:24:01 +0100

librg-utils-perl (1.0.19) stable; urgency=low

  * moved in runNewPSIC.pl from snapfun

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 19 Jan 2011 16:41:10 +0100

librg-utils-perl (1.0.18) stable; urgency=low

  * RG/Utils/Copf.pm: fixed sequence name issue with trailing '|'

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 11 Jan 2011 16:29:34 +0100

librg-utils-perl (1.0.17) stable; urgency=low

  * RG/Utils/Copf.pm: FASTA sequences can now consist of [A-Z.~_!-]

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 20 Oct 2010 09:57:21 +0200

librg-utils-perl (1.0.16) stable; urgency=low

  * RG/Utils/Copf.pm reported success (0) even when failed - corrected

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 07 Oct 2010 10:14:24 +0200

librg-utils-perl (1.0.15) stable; urgency=low

  * copf now uses a temporary directory for work dir if none given

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 29 Sep 2010 16:41:39 +0200

librg-utils-perl (1.0.14) stable; urgency=low

  * copf.pl lower case FASTA format recognition bug fixed

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 20 Sep 2010 17:16:21 +0200

librg-utils-perl (1.0.13) stable; urgency=low

  * Default is now not to change the nice level

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 24 Aug 2010 10:44:39 +0200

librg-utils-perl (1.0.12) stable; urgency=low

  * Fixed blast2saf log file issue

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 10 Aug 2010 21:31:43 +0200

librg-utils-perl (1.0.11) stable; urgency=low

  * Now tools die of errors instead of reporting success

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 24 Jun 2010 18:27:56 +0200

librg-utils-perl (1.0.10) stable; urgency=low

  * Silenced regular operation of copf.pl and hssp_filter.pl

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 17 Jun 2010 11:41:22 +0200

librg-utils-perl (1.0.9) stable; urgency=low

  * fileOutErr is now optional: will use STDERR if not given

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 17 Jun 2010 10:44:54 +0200

librg-utils-perl (1.0.8) stable; urgency=low

  * Better command failure detection and error reporting

 -- Laszlo Kajan <lkajan@rostlab.org>  Sun, 16 May 2010 00:29:42 +0200

librg-utils-perl (1.0.7) stable; urgency=low

  * Better command failure detection and error reporting

 -- Laszlo Kajan <lkajan@rostlab.org>  Sat, 15 May 2010 00:00:44 +0200

librg-utils-perl (1.0.6) stable; urgency=low

  * Added Mat to: next if ($kwd =~ /^file(In|Out|Help|Def|Mat)/i); # lkajan: infernal. This should be a next UNLESS /something/ condition.
  * added profphd-utils dependency
  * sed --in-place -> -i because Mac sed does not understand --in-place

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 12 May 2010 22:08:00 +0200

librg-utils-perl (1.0.5) stable; urgency=low

  * Added safFilterRed.pl from profphd

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 14 Jan 2010 20:44:49 +0100

librg-utils-perl (1.0.4) unstable; urgency=low

  * Corrected dirSrcMat path
  * Corrected package method calls by qualifying package properly
  * Added missing mat/Blast_blosum62.metric; added conv_hssp2saf.pl from profphd; fixed syntax error in hssp_filter.pl;
  * Fixed syntax error in hssp_filter.pl

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 14 Jan 2010 20:44:49 +0100

librg-utils-perl (1.0.3) unstable; urgency=low

  * Simpler repository organization

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 14 Jan 2010 11:50:24 +0100

