debian/changelog

-libucsc (0.0+git20180904.0e87e322+dfsg-1) UNRELEASED; urgency=medium
+libucsc (0.0+git20181204.8fcb9fa0+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #xxxxxx)
-  Does not build due to usage of htslib 1.3:
-    https://github.com/ucscGenomeBrowser/kent/issues/13
 
- -- Andreas Tille <tille@debian.org>  Sat, 19 May 2018 13:59:04 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 05 Dec 2018 11:38:35 +0100

debian/control

@@ -7,14 +7,16 @@ Build-Depends: debhelper (>= 11~),
                libhts-dev,
                libssl-dev,
                libpng-dev,
-               libmysqlclient-dev
-Standards-Version: 4.1.4
+               libmariadb-java,
+               uuid-dev
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/libucsc
 Vcs-Git: https://salsa.debian.org/med-team/libucsc.git
 Homepage: http://genome.ucsc.edu/
 
 Package: libucsc0
 Architecture: any
+Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: library used in ucsc genome browser
@@ -32,6 +34,7 @@ Description: library used in ucsc genome browser
 
 Package: libucsc-dev
 Architecture: any
+Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: library used in ucsc genome browser (development files)

debian/copyright

@@ -12,13 +12,15 @@ Files-Excluded:
     LICENSE
     README
     src/a*
-    src/b*
+    src/browserbox
     src/c*
     src/d*
     src/f*
     src/g*
     src/hca
     src/hg
+    src/htslib/config.log
+    src/htslib/config.status
     src/idbQuery
     src/index
     src/intronerator
@@ -34,8 +36,8 @@ Files-Excluded:
     src/t*
     src/w*
     src/x*
-    src/LICENSE
     src/README
+    */.gitignore
 Comment:  The LICENSE file in the root dir says:
  LICENSE files in subdirectories override the text of this LICENSE file.
 
@@ -59,7 +61,7 @@ License: MIT
  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-Files: lib/font/*
+Files: src/lib/font/*
 Copyright: 1984-1989, 1994 Adobe Systems Incorporated.,
            1988, 1994 Digital Equipment Corporation.
 License: Adobe
@@ -108,7 +110,7 @@ Comment:
  The license statement above was verified at
     http://cvsweb.xfree86.org/cvsweb/xc/fonts/bdf/100dpi/courR24.bdf?rev=1.3&content-type=text/vnd.viewcvs-markup
 
-Files: lib/font/mgSail8.c
+Files: src/lib/font/mgSail8.c
 Copyright: 2011 LatinoType Limitada <luciano@latinotype.com>
 License: SILOpenFontLicense
  PREAMBLE
@@ -213,7 +215,7 @@ Comment:  lib/font/README says:
     http://www.fontsquirrel.com/fonts/sail
  is most probably the source of the sail font
 
-Files: lib/font/mgSixhi6.c
+Files: src/lib/font/mgSixhi6.c
 Copyright: unknown
 License: unknown
  lib/font/README says:
@@ -224,6 +226,122 @@ Comment: Websearch to find back what was lost was not successful.  It
  can be assumed thst this single file can be distributed and the package
  is non-free anyway.
 
+Files: src/htslib/*
+Copyright: © 2012-2016 Genome Research Ltd.
+           © 2008-2013 Broad Institute / Massachusetts Institute of Technology
+           © The Wellcome Trust Sanger Institute
+           © 2008-2012 by Attractive Chaos <attractor@live.co.uk>
+License: MIT
+Comment: Asked upstream for compatibility to Debian packaged version
+   https://github.com/ucscGenomeBrowser/kent/issues/13
+
+Files: src/htslib/cram/*
+Copyright: © 2012-2014 Genome Research Ltd.
+           © 1995-2003 MEDICAL RESEARCH COUNCIL
+License: Various_BSD-3-Clause
+ The files in the 'cram' directory are under one or both of the following
+ licenses.
+ .
+ ---------------------------------------------------------------------------
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ Institute nor the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ .
+ ---------------------------------------------------------------------------
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1 Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2 Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
+ MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
+ promote products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: md5.c
+Copyright: No copyright is claimed
+License: solar-MD5
+ This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
+ MD5 Message-Digest Algorithm (RFC 1321).
+ .
+ Homepage:
+ http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
+ .
+ Author:
+ Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
+ .
+ This software was written by Alexander Peslyak in 2001.  No copyright is
+ claimed, and the software is hereby placed in the public domain.
+ In case this attempt to disclaim copyright and place the software in the
+ public domain is deemed null and void, then the software is
+ Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
+ general public under the following terms:
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted.
+ .
+ There's ABSOLUTELY NO WARRANTY, express or implied.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
 Files: debian/*
 Copyright: 2014-2018 Andreas Tille <tille@debian.org>
 License: Apache-2.0

debian/rules

@@ -16,4 +16,8 @@ include /usr/share/dpkg/default.mk
 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --sourcedirectory=src/lib
+	dh $@ --sourcedirectory=src/lib --no-parallel
+
+override_dh_auto_build:
+	make --directory=src/htslib
+	dh_auto_build

src/LICENSE

+Copyright (C) 2001 UC Regents
+
+LICENSE files in subdirectories override the text of this LICENSE file.
+
+Permission is hereby granted, free of charge, to any person or non-commercial
+entity obtaining a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including without
+limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom
+the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Commercial users should contact kent@soe.ucsc.edu for access to other modules
+including jkOwnLib and blat.
+
+Commercial users interested in the UCSC Genome Browser in particular please see
+    http://genome.ucsc.edu/license/.
+
+The code in /src/htslib is distributed with two licenses as noted in the LICENSE
+file in that directory.

src/blat/hCrea.geno

+>hCreaGeno
+CATGCCACATCCCCGGGGCGGGAGGGGGCTACATCCCCGGCTTTAGACGCGCGAGTCTCAGGTCCCGCTA
+ATTACCTGGCGGGTGCTGCCCACCCCTGCCCTCGCGCACCTAGCGCGTGGCAGCGGGAAGGCGGGGCCTG
+GGGGAGCCCCACCCCTGGAGACTGCGGCTGGGGCCTCCCTCTCCTCCGCCCGCCCGCCTGCCACTAGCTC
+ATTGCGCCTCTCCTGCAGTCTGATTGGGCACCGGCTCCCATTCCGGCTCCAGCCTCCAATCCGACCCCCA
+TTTCGGCTGCAGCCTCGGACCTAGCTCCGGCCCTCGGTCTATCCGGTTGCATCCTCCCTCCCTGTTCCGG
+ATCTTATCTTGCGCCAGCGCCTACTCCAGGATCCCGTAGCCAGACCTCAAGCCATGGCTGGTCCCTTCTC
+CCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGG
+TTTCTGCTCCGACCGGAACCTGTACGAGCTGCCAGTGAACGACGGAGGCTGTATCCCCCGAGGTAACAGT
+GCCTGAGGCGCGGGAGGAGGCGGGGGCAGGAGGTGATGGGAACGAAGGTGCGGGTAGAAGTGAGAATCCG
+GGCAACAGAGAAGGGCTATAATCACGAAGGCCCTGGAGCTGGAGGGCTGTGCAGTCTGCAGACCTCAGTG
+GGGTGGGGGTGGGGGCCAAAACCATAAAGCAAGAACATTCCTGGGGACCTGCCAAGACCAGCTCTGGCCC
+TACGAGTTCTAGCTGCACTGGCTGCCCAAATCCCTAATTGTAAAGCCAGGAACTATCCTTTTCGCTCCCC
+TCCATCTCCTTCCCTCATTTCCTCAATTCCTCTCCTTAGGCTTTTCCCCTCCTCCATCCGTAGTGTTGTG
+TCATGGGAGGAAAGAACTGAGCAGATCTGAAGAAACTGAGCTGGCCAGCCAGAGGCAACTAGAACTATTA
+GGAAAGCATAGACTCTGAAAGTCCCTAAAGAGATTACCAAGGTTTACCCTCTTTCTAATTCCCCTCCTCC
+CGCGGAGCAAAGCCAGACATGGCCAACTGGACAGCTCCCAGGTAACTGCACTAGGTCTAGGCGTCTGTGA
+CCCTCCCTCCATGGTTACTGGGTACCCCCTCCCCAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAAC
+TGCATGGCCAGTCACCTGACCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGA
+CGCTAGATCAGTGTATCCAGACTGGCGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGT
+GGCTGGAGATGAGGAGACCTATGAGGTAGGGGGTCCCCAGAGTCTCCCTGATGATCCAATTCATCTTCCC
+AGTAATCCCAGCTCCTTTCCCTTAAAGACCTCTCACTTTCCCCCAAGACTCTGAGCCCCCCATACTTAAG
+TTTTCTGAACCAGTGAAATCAATGCACAATTGAAGTCTGGGGAGGGATTCCCTCTCCTTAACCATCTCTC
+CCTCTTAACTCCCCTTAGGTATTTGCTGACCTGTTTGACCCTGTGATCCAAGAGCGACACAATGGATATG
+ACCCCCGGACAATGAAGCACACCACGGATCTAGATGCCAGTAAAGTGAGTTCAAATATCCCACTTCTGAT
+TTGCATTGCCTGTGTACAACACTCTGTATCTCCAACCCCTTCACCTTATTTCCTGACTCATGGTCATTAT
+ACTGCTGAGCTTTTAATCTTAATGTAAGGAAAGAATCATATCTTAAGGGGCAGCATATATGGAGATGGAA
+GGATAGATAAGAATGACCATGACCCAAGGTGGGTGGTTTGGGGACGGGTCTGCAATGCCCCCTTCAATTC
+CAGTGCTTTCCCAAAGGGCCTCTTCTTCCAATGCATGCAGGAAGAATGCACACAGAGTCCTCTAATGCCT
+AAGGAAGGTCTCTCCTTTCCCAGGGGCCCTCAGTTCCCACCGTGTTTCTGTGACTTACATTCATTTCCCT
+TATCTCCCAGATCCGTTCTGGCTACTTTGATGAGAGGTATGTATTGTCCTCTAGAGTCAGAACTGGCCGA
+AGCATCCGAGGACTCAGTCTGCCTCCAGCTTGCACTCGAGCAGAGCGACGAGAGGTGGAACGTGTTGTGG
+TGGATGCACTGAGTGGCCTGAAGGGTGACCTGGCTGGACGTTACTATAGGCTCAGTGAGATGACAGAGGC
+TGAACAGCAGCAGCTTATTGATGTGAGGGCCTTAAGAGGGTGCTGGTTGGTGGGAGCAGATGGGGAAGGC
+TGGGCCAGATGAGACATGGGCTCTGAAAGGCCCAGGGGCCACCATGAAGATTCTTAACCCAAGTCCCGTT
+ACTCTTCCCAGGACCACTTTCTGTTTGATAAGCCTGTGTCCCCGTTGCTGACTGCAGCAGGAATGGCTCG
+AGACTGGCCAGATGCTCGTGGAATTTGGTATGAAGCTGCTCATTACCTCTTTTGTCTTCATGCCCTCATA
+AATGCTTTTTTTCCCTCTATCTCTCCCAATTCTTGCCTTGCCTCTTGATCACTGTCCCTCTCCGGCCCTC
+AGGCACAACAATGAGAAGAGCTTCCTGATCTGGGTGAATGAGGAGGATCATACACGGGTGATCTCCATGG
+AGAAGGGTGGTAACATGAAGAGAGTGTTTGAAAGATTCTGCCGAGGCCTCAAAGAGGTTAGAGAAGACTA
+TGTAGGGGAGCTAGGTGGGAGGACATAAGGAAAACCAAAGAGTAGCATAAATAGATTATGTAATTTACCA
+ACCAACCCAGGACATGTCTTATAGTAAAAAGGACTATCTAGGACTCACTCCAGGACTAAAGGTGTAAACC
+AGCTGGGACCATACTGGGAAAACCAGGACATGTGGTCACACTAAGATTAGGAAAAGAAAGAGTGTCAGGA
+ATCTTAGGAAGTGAACAAGGCTTTTGACAGAGAGTGCAAAGAAGGAATAAATGAGATGGCACGTCAGTGC
+CTGGGATGTGTGCAGTGGGATGGTGAGGTGTGCAGATAAGGAAAACATTCGAGCTTAGATTGATGTTGGC
+GGGGAGAGGTTGCTGTGTTCATGACTCTAATATAACCACCCAGTTCTGAGACAAGGTAGGCCTTGACTCT
+GGATTCTATCATTCTTGTTAAAGTTTCGGGTCTAGGCTTTAAGTTGAGAGTTCGGAGAGAGACTGGGGAA
+GGTGGAGGATAGAATGGTTCGAGTTCTAGAATATGTGGCTCTAGATGAGAGGTTGAACTGAATCATCAAT
+CCTACATGGATTGGGTCTCCGTATTCAAGTCTACATTAGAAATCCCCATAAACTCAATTCAATTCTTACT
+GTATGTTCTCAAACATACAGTTCTATTTTAGGTTTGCAAAGAAAAAGAGCTCCTCTTTTAGATTCTGAGA
+AGTTTCTACTATTTTTGGCAAGTAATAGATAACATATTCTGACTATGAGTGGGtagggaagtacctttaa
+attatatgcctcagtttcctcatctgtaaaattgggataatgagattttctacattttaggttgttgtgg
+ggattaagtgaaatacaggtaaagtacttggtccacagtaagtgcttaataagtgttaaagtgttagctg
+caatattattCTGGATGGAAGAGTTTCCCCCCATGTTCAGCATGTAAGATATCCCCTATGGCATGGTTCC
+TTCTGAACTATAAAGAGGATCCCTTTACTCATGTTGGGTTGTGGTCTTTGTGACCATCATTCTGCTAGAT
+CCCTTGTCTCTTGAACTCTAATAGTCATCTTCATGACTACATGGTTAAGTGAAGCCAAACGCCTTCCCCC
+CGCCCCCTATTCCTATGAATCTGGCTTTTCTGCTCTGTTTTCATCTTTCTCTGCATTCACACAGGTGCTC
+CGTTCACAGCTAACAGAATGTTATCTTACCTCTTCCTGGCAAAGCTTACACCTTCATCTTCTGTCTGAAG
+GGACCCTTCTAAGCTCTAGGCTCATTAGCAAAGCAAAGATAATCGATGCATGCAGACCTCATTGAATAAT
+CAGTCATCTCTCAGTTCAGTTTACCACCTCTGTTCATTTCCCTAGATCATCCTTAATACACCACTCCTTC
+GAGTTTTCTTCTTCCACATAAGATATTTTTTCACAATCTCATTATTATGCACATCATAATTTTGCATCAT
+GCATGCATGAAAACAATAACAAACCTTTTTCATTTAAAAAAAGACCAATGTCATTCATTCACAGCCAAGT
+TTCTGTTCTAGACATATTTCTAGTGTTCTTGTGGGTCTAGCTAAGGGAGGGTCCAGGGTTAATGAAATAT
+CCCTGATTTTTCGTTAACAAAACCTTTGTGGACTCAGGTGGAGAGACTTATCCAAGAACGTGGCTGGGAG
+TTCATGTGGAATGAGCGTTTGGGATACATCTTGACCTGTCCATCTAACCTGGGCACTGGACTTCGGGCAG
+GAGTGCACATCAAACTGCCCCTGCTAAGCAAAGTAAAGGAGTTGTGGGGTTACAGAGGGGTGTGAGTAAG
+GAAGGGTGGGTTGTGGATGGGGAGGGAGTGGACCCTTTGGAAAGGAGCCAAACATGTTGTGGCTAAAGGG
+TCAGAGGACAggccaggcacagtggctcatgcctctaatcccaacacttgggaggccaaggcaggcagat
+tacttgagcccaggagttcaagaccagcctgggcaacctggtgaaaccccatctctacctacaaatacaa
+aagttagctgggtgtagtggaggctgaggtgagaggatcacttaagcctgggaagtcgaggcttcagtga
+gctgtgatcactccagcctgggtgacagagagagaccctgtctaaaaaaaattaaaaaagaaaaaagaaa
+aaaGGAAAAAAAAAGTTCAGGAGACAGAGCTCTGAGCAGGTTCAGGGCTCTTTCAGGTAGGACCTAGTCT
+CTGCCTCTATTGACCCTGCTCCCAATCCCTATCTCCTCTCTAGGATAGCCGCTTCCCAAAGATCCTGGAG
+AACCTAAGACTCCAAAAACGTGGTACTGGAGGAGTGGACACTGCTGCTACAGGCGGTGTCTTTGATATTT
+CTAATTTGGACCGACTAGGCAAATCAGAGGTGAGATCCTAAGGGATTAGGACAAGGAGAGGTATAGGTCT
+GCGAGGGCCGAAATATGGCAGTGAGTGAGCCTCCGGGATGTAACATAATCTGAAATGAAATTCAGGTTGA
+GTGGGAGGCAATTGGAAATGAGCAGGCAAGTCAGTCAGTGATAAAGAAAAACTCAGACTGTAGGAAGCAG
+ATCAAAGATTAGTGTCCCTTAGGTGGAGCTGGTGCAACTGGTCATCGATGGAGTAAACTATTTGATTGAT
+TGTGAACGGCGTCTGGAGAGAGGCCAGGATATCCGCATCCCCACACCTGTCATCCACACCAAGCATTAAC
+TCCCCATCGCCAGCTGATGACTCAAGATTCCCAGGAGTTTTGCTCATTCTAATGATGGCCCATTCTACTT
+GCTCTGGACCTGCCCCCGCATCCCCTGCCTCCATCCTAGTAAAGACTCCTTGCTATGCTGCAGCTGTCTG
+TGTTACTTCTAATGGTGGGGTGAGGAGGGAGCAGCCTTCAGGAAATGAAAAGAGGCAGTGGGATTATTTA
+TGATGGAAAGAGACTCCAGATATGGCAACCCAGGAACACTGATTCTCAGGTGGGTGGAAAGCATTAACAT
+TTTACCCATATTCCTCATCAGCTTCTGAAAATAATCAGGATGCACTTCTGTTTGCACTTTATTCATTATG
+ACTTAAGATTTCTCTCCCCACAATCTCCTTCTACTGTAGAGACAGGCTCATAGCAGGTGGCCAAGGAAGC
+TGATAGTCAATACCAGGGACCAGGAAGGTCGTGACCAGTCCTGGAGGCCCCAGGCTGTACTTCGACCTAT
+AATAGACAGGGAATGGGAGTAATATCACAACTCAGCTCTCCAGGAGCATTGATACTTGGAAATTAGCGCT
+CTGCCTGTAGACTCCTTCACTCCAGGGATCTCCCTGGGTGCACTCTAAGAGCCAGACAGCACCAAATTAG
+GGGTTTGATTCTGGGTCAGGAGATGGAGGATCAAGCTGTGCAGCTGGGAACTCACCTTGCTGTTCTGGGC
+TCTCCTTTCCCTCATGTTGGGCCCATGCAACTGCTCGTCGCTGCTCAGGACTCAGAAAGGCCATTTGCTC
+AGGAGTGACAGCCACAGCCTGAGCACTGGTGAGACTAGATAGTTGGATGGGACTAAACACCACCTGAGGG
+CAGGGGTAGGAATCAGTGCATGCATGTAGTCCCCATTGGGCCCTGGCTCTCCTGTGGTCACCCCAGTCCA
+TTAATACTTACAGCAAATTTAGGAGGAGGGATGACAGAAATGGCAAGAGGAGTAACGCCCTGGATCTGTC
+CCCGCAGCAGTGCTGAAAGAGCCAGGTCTGGGATCCCAGCTGTTGAAGCAAGTGGCATCCAAACATTGTC
+TTAGACTGACCTTCCCTCTCTTCAAACCTATAGACCTTCTCTAACTACTCCCAAAGTGCCCTATCATAGA
+CCTTCCCCAATATGTCTCTAGCCCCTTATTTAAACACCCTCAGGCCCCCACCTTAAGAATTGCAGGGCAG
+TCTTCCATCCAGTCCACCCATGGTATAGAAACCAAACCAACTTGCACCAGCAGTGGCCCAGCTCCCCACC
+TGCTATGGTGCCAATTTCAGTGAAGATCTCAGGCCCCCAGTTACTGATTGGGCCAAACCCACCAGGCAGT
+ACAAGTAGGTGGGCCAGAACCTCCAGTTGTTCCTCAGAGCACTGCAGATGCAGGGTGCCGAGGAAGAGAG
+CTGCTTGGCTGTAGAACAGTGGGAAGGAAGGAAGAA

src/blat/hCrea.mrna

+>hCreaMrna
+CCGGCTCCCATTCCGGCTCCAGCCTCCAATCCGACCCCCATTTCGGCTGCAGCCTCGGACCTAGCTCCGG
+CCCTCGGTCTATCCGGTTGCATCCTCCCTCCCTGTTCCGGATCTTATCTTGCGCCAGCGCCTACTCCAGG
+ATCCCGTAGCCAGACCTCAAGCCATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAG
+GCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCT
+GCCAGTGAACGACGGAGGCTGTATCCCCCGAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAACTGCA
+TGGCCAGTCACCTGACCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACGCT
+AGATCAGTGTATCCAGACTGGCGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGTGGCT
+GGAGATGAGGAGACCTATGAGGTATTTGCTGACCTGTTTGACCCTGTGATCCAAGAGCGACACAATGGAT
+ATGACCCCCGGACAATGAAGCACACCACGGATCTAGATGCCAGTAAAATCCGTTCTGGCTACTTTGATGA
+GAGGTATGTATTGTCCTCTAGAGTCAGAACTGGCCGAAGCATCCGAGGACTCAGTCTGCCTCCAGCTTGC
+ACTCGAGCAGAGCGACGAGAGGTGGAACGTGTTGTGGTGGATGCACTGAGTGGCCTGAAGGGTGACCTGG
+CTGGACGTTACTATAGGCTCAGTGAGATGACAGAGGCTGAACAGCAGCAGCTTATTGATGACCACTTTCT
+GTTTGATAAGCCTGTGTCCCCGTTGCTGACTGCAGCAGGAATGGCTCGAGACTGGCCAGATGCTCGTGGA
+ATTTGGCACAACAATGAGAAGAGCTTCCTGATCTGGGTGAATGAGGAGGATCATACACGGGTGATCTCCA
+TGGAGAAGGGTGGTAACATGAAGAGAGTGTTTGAAAGATTCTGCCGAGGCCTCAAAGAGGTGGAGAGACT
+TATCCAAGAACGTGGCTGGGAGTTCATGTGGAATGAGCGTTTGGGATACATCTTGACCTGTCCATCTAAC
+CTGGGCACTGGACTTCGGGCAGGAGTGCACATCAAACTGCCCCTGCTAAGCAAAGATAGCCGCTTCCCAA
+AGATCCTGGAGAACCTAAGACTCCAAAAACGTGGTACTGGAGGAGTGGACACTGCTGCTACAGGCGGTGT
+CTTTGATATTTCTAATTTGGACCGACTAGGCAAATCAGAGGTGGAGCTGGTGCAACTGGTCATCGATGGA
+GTAAACTATTTGATTGATTGTGAACGGCGTCTGGAGAGAGGCCAGGATATCCGCATCCCCACACCTGTCA
+TCCACACCAAGCATTAACTCCCCATCGCCAGCTGATGACTCAAGATTCCCAGGAGTTTTGCTCATTCTAA
+TGATGGCCCATTCTACTTGCTCTGGACCTGCCCCCGCATCCCCTGCCTCCATCCTAGTAAAAAAAAAAAA

src/blat/hCrea.pep

+>hCreaPep
+MAGPFSRLLSARPGLRLLALAGAGSLAAGFLLRPEPVRAASERRRLYPPSAEYPDLRKHNNCMASHLTPA
+VYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYEVFADLFDPVIQERHNGYDPRTMKH
+TTDLDASKIRSGYFDERYVLSSRVRTGRSIRGLSLPPACTRAERREVERVVVDALSGLKGDLAGRYYRLS
+EMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNMK
+RVFERFCRGLKEVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHIKLPLLSKDSRFPKILENLRL
+QKRGTGGVDTAATGGVFDISNLDRLGKSEVELVQLVIDGVNYLIDCERRLERGQDIRIPTPVIHTKH

src/blat/mCrea.geno

+>mCreatGeno
+GAATTCATCAAGGGATAAATCCATTAATTAGAGTAGAGCCCTTTTGAGCTTTTTGCAATAGCTGGTAATT
+AACCAAACCCCAATACATGAGCCAGTAAAGAACATTTCTTATCGAAAAAGAATTGATGATACTGATGATA
+TGAAAGCTTATTTACGCATATGTTACTGTTGACCTTGAATCTTCATTTAGGAGTTTGAGTGCCCCCATTT
+GTTCTCTATAATTTTGGGAACCTAGGAATTGTCCTAGTTAGATGCCTCATCTTACTGAAACCTCTGCCCC
+AGGCTTCCTGAATTGATAGAGATAGATTCTAAGAGCAGAATCTACAAAGAATCAGTGATAGTTAGGGCTC
+AGACTCATTCCTCTTCTACCACTCCAACCCTGGGAGCGAGTAATTACCGCAGCTCCCAGCTGTAAACAGC
+CTCCAGCGACCCCACTGGCATACTGAGCCTCACAAAGAATTTAAAAAGTGCACAAATCGATGAGCCCTCT
+TGGAAGAGCTATTGTTTCCCATAGGAAGGCATTTNCCAAATTTGAATGACTTCTCTGTACCCTGGCTGCC
+TTTACTTCTTCTGTTAGCCTCTCTTCCCACACCCCACTCCTGAACACCTTCTCAGCCAAATAATAGCCCA
+ATTGCTCTCGAAGACTATCTCCTCCTTTTATCTGGGTAAATATCNCCATCCCAAGTAATTATATCACTTA
+CTCATACCTCNCCTTACCTGGATATGAACACCCACAGCACAGGTAACATTTTTTTTCCCTCTCCAAAAAT
+AAGGAAGTTCCACCAGTAGATCTCTATCTTGGAAAATGTGTTATGTTACCAAGAGAAGAGGCTTAAGTAA
+TGGAGCCAAAAGTGAAATGGATTCTTTCTAAGGATACNCACCAATGAGAAAGGTCAGAAAGGAGACATAT
+GGGGTGGGGACTTGAGGGAAATAATTAATGTATATAGTTGGGCCAGTGGGGATTATGAAGGGTAATTCTT
+TTTCCCAAGTACTTTCTTACAACTTCCAAATATCTTACTGTCTTCTGGAACATCAGGAAGCTGAAGGTAG
+ACATATTAANNNCAATATGTCTGCTTTTGCTTTGGCTGGCCCTCCGCACCCAAACCTCAGGTCTCTATCT
+CAGCTTCAGCTTTCATTCCCCTTCCCAATATGTCTGCTTTGCTTTGGCTGGCCCTCCGCACCCAAACCTC
+AGGTCTCTATCTCAGCTTCAGCTTTCATTCCCCTTCCTGCACTAATAAAAGTCAAGTTGCTCCTAGCCCA
+GCACGTAGCTGTGGAAACAAACCCTCTTGAGTCTGAGTATGCACTTCGCAAAAGAGAGAGCGGACCAGGA
+AGAAGACAGAGACTCCCTGATGACCTTATGCCCTTGGATACTACCAGCCTTCACACTCCAGTTTAAACTG
+CCTTAGCAAGCCAAGAGAGGAAGCACGAGTGGTTCGGGAGACCTGTGCCTGCCTGTTCCATTCCACACCC
+AGTCATCTCACCAGACCCTCCTCCTCTCTTTATATTCCCCCTCCAGTCCTAGGAACTGCCAGCTGCAGAG
+AAGAAGGAAGAGAAGGAAGAAGAAACTCACCATTCCCTGCCCAACCCCAGCCCCACACCCAGAGCAATCA
+ACAGGTAGGCTTTCAGACACTACTCAGGAAGAGTCCTTCGAACAGCAAACAGATTTAAGCCTGGAAAAGA
+AGAAGAGAAATAAAAGATCAAAGGTGAAGCAGGGGTTAGAGTAGAGGAAAAAAAGAAAAAAAAAGCAGGT
+CCCCAATGAGAGGCAGGAAATAGCCAAGCTGAAGACTTGGAGGCAGTGAGTTTGGGAGACAGGATTCTTA
+AGGGATCCTTTCTCGACCTTATTAGGAAAGCATAGGTGTAGCTGGAGTTCCCTGGTGCTTCCTGGTTCTT
+AGGGAAGGTGACTTGAGGCTGTGCTGTCTTTCCCCTGAGCTCGCTCAGTCTTCCTCCTCTATCTGTTTAT
+TCTGTGGTTTTCCTGCGGCTGACTCTCCTGGGGAAAATGGAGAGATGGCGTGCAGATCGAATTCAATTCA
+GAAAAGAGGCTGGGCAATGTCAACCTCCCCACCCCCACCCCCAAAACCCAGAAATAGACGGATTGGTTTC
+AGATTTAAACAGAGAGGGTATGAAAGAAGGGGGGTTTCAGGTTCGGGAATCCCCGTGGTGCTGTCCTCTA
+CTTAGTGCTGAAATCTGACACCCTCATCCTTGGTGGGCGTCTGTCTCCAGCCTCAGGGAGTAAATCTCCA
+GTCTTCTTAATTACCTGGCTAGTGCTACCCAACCCCACCCCCGCACACCTAGCGCGGTGGCAGGCGGGAA
+GGCGGAGCCTGAGTGAGCCCCACCCCTGGAGACTGCGGCTGGGGCCTCCCTCTGCTCTGGCTGGCTCCTT
+GCTTCGCTGCGCTTCTCCTGCAGCCTGGTAGGCACCGGCTGCCACTTCAGCTTCAGCCTTCATCGTGACC
+CCTATTTTGGCTCCAGTCTCCGACCCAGCTCCGTCCTCTCTCTACCCGGTTGCATCTTCCCTCCTAGTTC
+CTGACTTGCACCAGATCCTGCTCTGAATCTTTGTAGCCGCATCCCCAAGCCATGGCTGGTCCCTTCTCCC
+GTCTGCTGTCTGCCCGCCCTGGACTCAGGCTCCTGGCTTTGGCTGGAGCTGGGTCTCTCACCGCCGGGAT
+TCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTGTATCCCCCGAGGTATTAG
+AGCCTGAGATGCACGAGGTGGGGGCTGGGGGTGGTAGTGGTGGTGATGGGAACCGAACAGGTAGAGAGGA
+TAACCTGAGCAAAAGATAGGCCTCGAAGATGGATTTCCTGTACAGTTTGGAGATCCTAGCCCTGTAATGG
+AAGAACATGTCTAAGGACATGTCACCCGATGTCACTGCCTCCACACCAGCTTTACCTTTGCAAATTCTAG
+GTTCACCCACTGCCCAAATCCTTTTTGGATGACTAGAAGCTTTTTTTTTTTTTTTTTTTTTTTAATCTCG
+ACCTATTCTCCTTGTTCTCCCGAATTCTCCTGAGTCTCTCCCCTCCCCCATCTCTAATGTTATGCTCACT
+AGAGAAAAGCAACTCTGTAGACAAGGGGGAATTGAGGTGTTAGAACTATTAGGAAAGAAAAGACCCTGGA
+AATCCCTGAAGAGATTATCAAGATTTAGCCTACCTCTAATTCCCCCTCCTTCCAATAAGCAAAGCCAGAC
+ATGGCTCACTGGACAGCTCCCAGCTGACATCAGTAGGTCTAGGCTCCTGTGCCCTCCCTCCATGGTTACT
+GGGTACCCCCTTCCCAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAACTGCATGGCCAGTCACCTGA
+CCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACACTAGATCAGTGCATCCA
+GACTGGAGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGTGGCTGGAGATGAGGAGACC
+TATGAGGTAGGGGGCCCCTCAGAAATCCCAGTTCCTTCCTCCTAAAGATCCCTCATGTCTGTTCCCTCAA
+GACTCTGGATTGTCTATACTCAAACGTTCTGATCCAGTGATATCAATCTACAACTCAAGTGTTTCTTCTT
+TATAATCGCCTCTTCCTCTTAACTCCTTTTCAGGTATTTGCTGAACTGTTTGACCCTGTGATCCAAGAGC
+GGCATAATGGATATGACCCCAGAACAATGAAGCACACCACTGACCTTGATGCCAGTAAAGTGAGCCAAAT
+GTGACACTTCCGATATGTGCAGCCTTGTGCACAATGTTCTGTATCTCCAATCATTACACCTTGTTTCCTG
+ACTCAGGGTTAGACTGCTGAGCTTTGTATATTGATAAGAGAAAGAATTGCATATCTTGAAGTATAGCAGA
+TAGGAGGACGTAGTGGATAAGAGTCTGGATAATGGAGTTGAGGAGAATCTGATCAAAGTACAAAATGGTG
+AAAGAATTTTTAAGAAGTGACTATGTCCTGGCTGGGTGTGGTGGCTCACACCTGTAATCTCAGCTCTCAG
+ACGGCTCAGAAGAGCACTCCTCCCTCCACCAAAAAAAAAAAAAAAAAGGCTGTACCCAAAGTGAGAAATG
+TGGAGAAATGACCACAGTGTTTTCAGTTAGCATGCCTGTCCAATGTGTCTTCCTTCTGGCACCTGCTTTA
+TAATCCCCAAGAGTTCCCACCTGCTGTGTTTCTATGATTTATAGTCATTTCTCTTATTCCTCAGATTCGT
+TCTGGCTACTTTGATGAGAGGTATGTATTGTCTTCAAGAGTCAGAACTGGCCGAAGTATCAGGGGACTCA
+GTCTCCCTCCAGCCTGCACTCGGGCAGAGCGAAGAGAGGTAGAACGTGTTGTGGTGGATGCTCTGAGTGG
+CCTGAAGGGTGACCTGGCTGGACGGTACTATAGGCTCAGTGAGATGACGGAGGCCGAACAGCAGCAGCTT
+ATTGATGTGAGGGCCTTGACAGGGAACGGGATTGTGGAAAAAGAGGTGGAGGGGAGAGTGGACCAGAAAA
+GGTAGATGGCCTGGATGGTACTGTGAGAATTCTTAGACCCAATCCCTTTATTCTCCTCAGGACCATTTTC
+TGTTTGATAAACCTGTGTCCCCATTGCTGACTGCAGCAGGAATGGCTCGAGACTGGCCTGATGCTCGAGG
+GATCTGGTATGGAGCCAACACACTTTTTTGGTTTTTTTTTTCCCCCTTGTATGTGCAAAGTTTTTTCTCC
+ATCTACCCCAGTGCTTGTCTTGCCCACTGATGGCTATACCTATCCTGCCCTCAGGCACAACAATGAGAAG
+AGTTTCTTGATCTGGGTGAATGAGGAGGACCACACACGGGTCATCTCTATGGAGAAAGGCGGCAACATGA
+AGAGAGTGTTTGAAAGATTCTGCCGGGGCCTCAAAGAGGTTGGAGAAGGGTATACCAGGGAGCTAGGGGA
+GAGGAAATGAGAAATACCACACAGCAGCATAGCTAGATCGGCTATATCACTTGTCAGTCAACCCAGAGTA
+TTTCTGATAGTAGAAAGGGTCATTATCATGCTAGGATAATAGTTACAAACCAGGGCCGTCCTTGGNAAAC
+CAGGGCATATAGTTACTCTAAAAATAGAAAGAGTGTCAGTAACCTAAGGAAGGAAATAAAGCATAATCTT
+TGCCAAGTAATGAAAAGAAGGAACCAATGATCAGCAAGCCAGTGCCGGGGTAGGTGGTATGAGGTAGTAT
+GTGCAGTTAAGGAGAACGTTTGAGCCTGGACTGATGGAAGGCGTGAGAGATTGGTTTGTTCATGATACAT
+CACCAAGTTCTGANCAAGGCTCACCTTGGCTCTGGAGATCTGATCCTTGATGTATTTTCTTGTATCTACA
+GTTTTATTTTTGGACTTGTAAAGAAAGGGTGCTTCTCTTTTAGATTCTAGCCAGGAAGCTCACACTATTT
+TCGGCAAGGAATGGATAATGTTCTATGAGTAGCATAGAGAAATACTCTTTAATTATATGACTCTGTTTAT
+TTGTCTATAAAGTTGAGGACTAAATGAAATAATGTAGGCAGAGGAATTGTTCTATAATAAGTGTTAGCTT
+TACGATGTAAAAATCTCCATGCTTGTGATTCCTTCTGAGTTACAGAGCATCATCTTTAGGTAGTGTGGTC
+TTTGTGTCTATTGCTCTGGCAGGCCCCTGTCTCTTCCATCCTAATAGTCATTATGGTGGTCAGGAAAGCA
+AGAACATCTCTTGAAGTCCCCCTCTTCTCACATGTACCTGTGAATCTGGCTTCTCTGCTGTACCTTCTCA
+TGTCTCCCTGCTCTATTATCCATGTTCCTTTTATAGCTAAGAGTAGGCTCTCCTGCCTTAGCACCTCGTT
+TCTGTCCAAAGGGACCCTTTGTCAAAGATGTAATTGATGCATGAGAACTCCCTGTCCTGTTTACTACTTC
+TATTCATTTCCCAAGTCACTCTTAATGTATCATTCTCCAAAGCTTCTTCTACGAACAATCTATCTGCCAC
+AATCTTATCAGCATGCATATAATGCAACATCCAAGTGTCCTTCCATGTGCAATGACAATAAGTTTTAACA
+ACAACAAAGAGCATGTCATTCATCGATCGTCAAGTTTCTCGTTGTAGACATAGTTCTAGAATGTCTGTGG
+GGCTAAGAGGGATCCCTCCCTCCCTGATTTTTCACAACAGAACCTCTGTTGACACAGGTGGAGAAGCTGA
+TCCAGGAACGAGGCTGGGAGTTCATGTGGAATGAGCGTTTAGGCTACATCTTGACCTGTCCATCTAACCT
+GGGCACTGGACTTCGGGCAGGAGTCCACATCAAACTGCCACTGCTGAGCAAAGTAAAGGATATGTGGGGC
+TAGAGGGGGTGTAAGAAGGGGGACTTGGAAGGGGGTGGAGGAGACACTCTAAAAAGAGCCAGTCCTAAGG
+GCTTATGGCTAGTGGGCCAAGGGTAGGAGCAGTCTCAGAAACTATTGACATGCCCCTGATCTTTACCTTG
+CATCTAGGATAACCGCTTCCCAAAGATCCTGGAGAACCTAAGACTGCAAAAGCGTGGAACTGGAGGAGTG
+GACACTGCTGCTACAGGCAGCGTCTTTGACATCTCTAATTTGGATCGACTTGGCAAGTCAGAGGTGAGGT
+CTTATGAATCAGGTTAAGAGGTTGAGATAAGGCAGTGAGTGAGCCTCAGGAACATAATAGAATCTGAAGC
+AATGGTCAGGTTGAGTGGGGTAGGGAAGAGAAAACGAGTTTTCAGAGATGGAAGAGCTAAAGAAACTCAG
+GTCAGGCAAGGTGGTCTGTGCTTTTAATACCAGCAGAAGCAAGACAGATCTCTGTGAGTCTCAGGCCAGC
+CAGGGCTACATAATGAGATCCTGTCACAAAAACTGAAAAAAGAAAAAGAAGGAAAAGAAGGAAGGAGGGA
+AGGAAGGAAGGGAGAGAGAGAGAGAGGGAGGGAGAGAGAGGAAGAGAGAGAGATTAAGAGAAGCTCGGGT
+ACACCGGGAAGCAGGGATCAAGGACTGTGTTCTTCAGGTGGAGCTGGTGCAGCTCGTCATCGATGGGGTG
+AACTATTTGATTGACTGTGAACGGCGTCTGGAGAGAGGACAGGATATTCGAATCCCTCCACCTCTTGTCC
+ACAGCAAACATTAACTCCCCATCCCCAGCGGATGAGTCAAGACCCCCAGGACTTCTGCATATTTAACAGT
+GGCCCAGTCTACTTGCCCTGGACCTGCCTCTCTCCCTGTCCTAGTAAAGACTCCACATTATGTTGCAGCT
+GTCTGTGTTATTTCTATTGGTGTGGTGAGGAGGAAGTAGGAAATGAAAAGAAACAGTGAGGTTATTCATG
+ATGGCAAGAGGCGTATATGCCAGGAGCACAGTTCTCAGGTGGGTGGAATGCATTGGAATTTTACCCACAA
+TCCTCATCCACTTACTGAGAATAATTAGTATGCACTTCCATTTACAAGTTGTTCAGTATGATGTAAATTT
+TCTCCCTCAACTGAAGGAACAGTTATCATAATAGGTGGCCAAAAAAAATGCTGACGGGGCAATGCCAGGG
+CCCAGGAGGCTTGGAACCAGTCGTAGAGACCCCAGGCTGAGTTTCGACCTAGAATGAGACAAGGAATGGG
+AGGAAAAAAAATCACAGTTCCGTTCCCCAGGAGCCTTTGATGTTTCAAATTTAGCTCTGTGTATAGATCC
+CTCTACTCCAGAGATTCTCCTGTGTGGGGTCTGAGGACCAGACAGCACCAAGTTAGGACTTAGATGGACT
+CTGGGTCAGATGACAGCTTATCAAACTATGCAGTTGGTAACGTACCCAGCTGCTCTGGGATCTCCTTCCC
+TTCGTGTTGGGCCC

src/blat/mCrea.mrna

+>mCreaMrna
+TGCTCTGGCTGGCTCCTTGCTTCGCTGCGCTTCTCCTGCAGCCTGGTAGGCACCGGCTGCCACTTCAGCT
+tcagccttcatcgtgacccctattttggctccagtctccgacccagctccgtcctctctctacccggttg
+CATCTTCCCTCCTAGTTCCTGACTTGCACCAGATCCTGCTCTGAATCTTTGTAGCCGCATCCCCAAGCCA
+tggctggtcccttctcccgtctgctgtctgcccgccctggactcaggctcctggctttggctggagctgg
+GTCTCTCACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTG
+tatcccccgagcgctgagtacccagacctccgaaagcacaacaactgcatggccagtcacctgaccccag
+CAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACACTAGATCAGTGCATCCAGACTGG
+agtggacaaccctggccaccccttcatcaagactgtgggcatggtggctggagatgaggagacctatgag
+GTATTTGCTGAACTGTTTGACCCTGTGATCCAAGAGCGGCATAATGGATATGACCCCAGAACAATGAAGC
+acaccactgaccttgatgccagtaaaattcgttctggctactttgatgagaggtatgtattgtcttcaag
+AGTCAGAACTGGCCGAAGTATCAGGGGACTCAGTCTCCCTCCAGCCTGCACTCGGGCAGAGCGAAGAGAG
+gtagaacgtgttgtggtggatgctctgagtggcctgaagggtgacctggctggacggtactataggctca
+GTGAGATGACGGAGGCCGAACAGCAGCAGCTTATTGATGACCATTTTCTGTTTGATAAACCTGTGTCCCC
+attgctgactgcagcaggaatggctcgagactggcctgatgctcgagggatctggcacaacaatgagaag
+AGTTTCTTGATCTGGGTGAATGAGGAGGACCACACACGGGTCATCTCTATGGAGAAAGGCGGCAACATGA
+agagagtgtttgaaagattctgccggggcctcaaagaggtggagaagctgatccaggaacgaggctggga
+GTTCATGTGGAATGAGCGTTTAGGCTACATCTTGACCTGTCCATCTAACCTGGGCACTGGACTTCGGGCA
+ggagtccacatcaaactgccactgctgagcaaagataaccgcttcccaaagatcctggagaacctaagac
+TGCAAAAGCGTGGAACTGGAGGAGTGGACACTGCTGCTACAGGCAGCGTCTTTGACATCTCTAATTTGGA
+tcgacttggcaagtcagaggtggagctggtgcagctcgtcatcgatggggtgaactatttgattgactgt
+GAACGGCGTCTGGAGAGAGGACAGGATATTCGAATCCCTCCACCTCTTGTCCACAGCAAACATTAACTCC
+ccatccccagcggatgagtcaagacccccaggacttctgcatatttaacagtggcccagtctacttgccc
+TGGACCTGCCTCTCTCCCTGTCCTAGTAAAGACTCCACATTATGTTGCAaaaaaaaaaaaaaaaaa

src/blat/mCrea.pep

+>mCreaPep
+MAGPFSRLLSARPGLRLLALAGAGSLTAGILLRPESVGAAAAERRRLYPPSAEYPDLRKHNNCMASHLTP
+AVYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYEVFAELFDPVIQERHNGYDPRTMK
+HTTDLDASKIRSGYFDERYVLSSRVRTGRSIRGLSLPPACTRAERREVERVVVDALSGLKGDLAGRYYRL
+SEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNM
+KRVFERFCRGLKEVEKLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHIKLPLLSKDNRFPKILENLR
+LQKRGTGGVDTAATGSVFDISNLDRLGKSEVELVQLVIDGVNYLIDCERRLERGQDIRIPPPLVHSKH

src/blat/makefile

+kentSrc = ..
+include ../inc/common.mk
+
+L += -lm $(SOCKETLIB) -lz
+MYLIBDIR = ../lib/$(MACHTYPE)
+MYLIBS =  $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a 
+
+O = blat.o
+
+blat: $O $(MYLIBS)
+	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
+	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
+
+all:
+	cd ../lib && ${MAKE}
+	make
+tags:
+	ctags *.c *.h ../lib/*.c ../inc/*.h
+
+test::
+	blat -verbose=0 hCrea.geno hCrea.mrna testRna.psl
+	cmp testRna.psl refRna.psl
+	blat -verbose=0 -prot hCrea.pep mCrea.pep testProt.psl
+	cmp testProt.psl refProt.psl
+	blat -verbose=0 -t=dnax -q=prot hCrea.geno mCrea.pep testProtX.psl
+	cmp testProtX.psl refProtX.psl
+	blat -verbose=0 -t=dnax -q=rnax hCrea.geno mCrea.mrna testRnaX.psl
+	cmp testRnaX.psl refRnaX.psl
+	blat -verbose=0 -fine hCrea.geno hCrea.mrna testFine.psl
+	cmp testFine.psl refFine.psl
+	cd test && ${MAKE}
+
+clean::
+	rm -f testRna.psl testProt.psl testProtX.psl testRnaX.psl \
+	testFine.psl $(O) blat

src/blat/refFine.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1531	0	0	0	0	0	8	3802	+	hCreaMrna	1540	0	1531	hCreaGeno	6896	240	5573	9	312,199,96,222,86,124,135,126,231,	0,312,511,607,829,915,1039,1174,1300,	240,1156,1558,2040,2391,2592,4377,5013,5342,

src/blat/refProt.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+370	9	0	0	0	0	0	0	+	mCreaPep	418	39	418	hCreaPep	417	38	417	1	379,	39,	38,
+38	7	0	0	0	0	0	0	+	mCreaPep	418	0	45	hCreaPep	417	0	45	1	45,	0,	0,

src/blat/refProtX.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+399	15	0	0	1	4	8	3811	++	mCreaPep	418	0	418	hCreaGeno	6896	403	5456	9	45,68,32,74,29,41,45,42,38,	0,49,117,149,223,252,293,338,380,	403,1151,1558,2040,2391,2593,4377,5013,5342,

src/blat/refRna.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1531	0	0	0	0	0	8	3802	+	hCreaMrna	1540	0	1531	hCreaGeno	6896	240	5573	9	312,199,96,222,86,124,135,126,231,	0,312,511,607,829,915,1039,1174,1300,	240,1156,1558,2040,2391,2592,4377,5013,5342,

src/blat/refRnaX.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1219	114	0	0	2	56	9	3865	++	mCreaMrna	1606	200	1589	hCreaGeno	6896	394	5592	10	145,205,96,222,82,128,135,126,167,27,	200,355,560,656,878,960,1088,1223,1349,1562,	394,1150,1558,2040,2391,2588,4377,5013,5342,5565,

src/blat/test/badSplice/small2.fa

+>Y14441 1
+gctggctcgagcctctcctgctcagcaccatggctaagacccctagtgac
+catctgctgtccaccctggaggagctggtgccctatgacttcgagaagtt
+caagttcaagctgcagaacaccagtgtgcagaaggagcactccaggatcc
+cccggagccagatccagagagccaggccggtgaagatggccactctgctg
+gtcacctactatggggaagagtacgccgtgcagctcaccctgcaggtcct
+gcgggccatcaaccagcgcctgctggccgaggagctccacagggcagcca
+ttcaggaatattccacacaagaaaacggcacagatgattccgcagcgtcc
+agctccctgggggagaacaagcccaggagcctgaagactccagaccaccc
+cgaggggaacgaggggaacggccctcggccgtacgggggcggagctgcca
+gcctgcggtgcagccagcccgaggccgggagggggctgtcgaggaagccc
+ctgagcaaacgcagagagaaggcctcggagggcctggacgcgcagggcaa
+gcctcggacccggagcccggccctgccgggcgggagaagccccggcccct
+gcagggcgctagaggggggccaggccgaggtccggctgcgcagaaacgcc
+agctccgcggggaggctgcaggggctggcggggggcgccccggggcagaa
+ggagtgcaggcccttcgaagtgtacctgccctcgggaaagatgcgaccta
+gaagccttgaggtcaccatttctacaggggagaaggcgcccgcaaatcca
+gaaattctcctgactctagaggaaaagacagctgcgaatctggactcggc
+aacagaaccccgggcaaggcccactccggatggaggggcatctgcggacc
+tgaaggaaggccctggaaatccagaacattcggtcaccggaaggccacca
+gacacggctgcgagtccccgctgccacgcccaggaaggagacccagttga
+cggtacctgtgtgcgtgattcctgcagcttccccgaggcagtttctgggc
+acccccaggcctcaggcagccgctcacctggctgcccccggtgccaggac
+tcccatgaaaggaagagcccgggaagcctaagcccccagcccctgccaca
+gtgtaagcgccacctgaagcaggtccagctgctcttctgtgaggatcacg
+atgagcccatctgcctcatctgcagtctgagtcaggagcaccaaggccac
+cgggtgcgccccattgaggaggtcgccctggaacacaagaagaaaattca
+gaagcagctggagcatctgaagaagctgagaaaatcaggggaggagcagc
+gatcctatggggaggagaaggcagtgagctttctgaaacaaactgaagcg
+ctgaagcagcgggtgcagaggaagctggagcaggtgtactacttcctgga
+gcagcaagagcatttctttgtggcctcactggaggacgtgggccagatgg
+ttgggcagatcaggaaggcatatgacacccgcgtatcccaggacatcgcc
+ctgctcgatgcgctgattggggaactggaggccaaggagtgccagtcaga
+atgggaacttctgcaggacattggagacatcttgcacagggctaagacag
+tgcctgtccctgaaaagtggaccactcctcaagagataaaacaaaagatc
+caactcctccaccagaagtcagagtttgtggagaagagcacaaagtactt
+ctcagaaaccctgcgttcagaaatggaaatgttcaatgttccagagctga
+ttggcgctcaggcacatgctgttaatgtgattctggatgcagaaaccgct
+taccccaacctcatcttctctgatgatctgaagagtgttagacttggaaa
+caagtgggagaggctgcctgatggcccgcaaagatttgacagctgtatca
+ttgttctgggctctccgagtttcctctctggccgccgttactgggaagtg
+gaggttggagacaaaacagcatggatcctgggagcctgcaagacatccat
+aagcaggaaagggaacatgactctgtcgccagagaatggctactgggtgg
+tgataatgatgaaggaaaatgagtaccaggcgtccagcgttcccccgacc
+cgcctgctaataaaggagcctcccaagcgtgtgggcatcttcgtggacta
+cagagttggaagcatctccttttacaatgtgacagccagatcccacatct
+atacattcgccagctgctctttctctgggccccttcaacctatcttcagc
+cctgggacacgtgatggagggaagaacacagctcctctgactatctgtcc
+agtgggtggtcaggggcctgactgaatgcccaacactgcatctctcttcc
+tgcttctggccttgtatcttgcattcacactcaatagtcacggaatgccg
+actaggtgctagctgctatgggaaatgcaaaaataacaaaatagttactg
+tgcccacggagcctacccgattatagcagaggtaagttaggaacgaacat
+gttagtcaatccgggtgaagacatgtactgatgacacaccatggatttca
+gaggaggaagtacggagtcgttgcataatccgcccctggtgggtggcact
+ctcaggtgctcctgaacagaagatttggccctcattttccctcagaaccc
+cacggcaaggatatatgtccccttgttctctctgcttctgtcttgaggat
+atgggaagcctagagaaacgcaagcagactggattgggatagaagtattt
+gtgtacctggattaatgaactatga
+>BC101511 1
+gctcgagcctctcctgctcagcaccatggctaagacccctagtgaccatc
+tgctgtccaccctggaggagctggtgccctatgacttcgagaagttcaag
+ttcaagctgcagaacaccagtgtgcagaaggagcactccaggatcccccg
+gagccagatccagagagccaggccggtgaagatggccactctgctggtca
+cctactatggggaagagtacgccgtgcagctcaccctgcaggtcctgcgg
+gccatcaaccagcgcctgctggccgaggagctccacagggcagccattca
+ggaatattccacacaagaaaacggcacagacgattccgcagcgtccagct
+ccctgggggagaacaagcccaggagcctgaagactccagaccaccccgag
+gggaacgaggggaacggccctcggccgtacgggggcggggctgccagcct
+gcggtgcagccagcccgaggccgggagggggctgtcgaggaagcccctga
+gcaaacgcagagagaaggcatcggagggcctggacgcgcagggcaagcct
+cggacccggagcccggccctgccgggcgggagaagccccggcccctgcag
+ggcgctagaggggggccaggccgaggtccagctgcgcagaaacgccagct
+ccgcggggaggctgcaggggctggcggggggcgccccggggcagaaggag
+tgcaggcccttcgaagtgtacctgccctcgggaaagatgcgacctagaag
+ccttgaggtcaccatttctacaggggagaaggcgcccgcaaatccagaaa
+ttctcctgactctagaggaaaagacagctgcgaatctggactcggcaaca
+gaaccccgggcaaggcccactccggatggaggggcatctgcggacctgaa
+ggaaggccctggaaatccagaacattcggtcaccggaaggccaccagaca
+cggctgcgagtccccgttgccacgcccaggaaggagacccagttgacggt
+acctgtgtgcgtgattcctgcagcttccccgaggcagtttctgggcaccc
+ccaggcctcaggcagccgctcacctggctgcccccggtgccaggactccc
+atgaaaggaagagcccgggaagcctaagcccccagcccctgccacagtgt
+aagcgccacctgaagcaggtccagctgctcttctgtgaggatcacgatga
+gcccatctgcctcatctgcagtctgagtcaggagcaccaaggccaccggg
+tgcgccccattgaggaggtcgccctggaacacaagaagaaaattcagaag
+cagctggagcatctgaagaagctgagaaaatcaggggaggagcagcgatc
+ctatggggaggagaaggcagtgagctttctgaaacaaactgaagcgctga
+agcagcgggtgcagaggaagctggagcaggtgtactacttcctggaacag
+caggagcatttctttgtggcctcactggaggacgtgggccagatggttgg
+gcagatcaggaaggcatatgacacccgcgtatcccaggacatcgccctgc
+tcgacgcgctgattggggaactggaggccaaggagtgccagtcagaatgg
+gaacttctgcaggacattggagacatcttgcacagggctaagacagtgcc
+tgtccctgaaaagtggaccactcctcaagagataaaacaaaagatccaac
+tcctccaccagaagtcagagtttgtggagaagagcacaaagtacttctca
+gaaaccctgcgttcagaaatggaaatgttcaatgttccggagctgattgg
+cgctcaggcacatgctgttaatgtgattctggatgcagaaaccgcttacc
+ccaacctcatcttctctgatgatctgaagagtgttagacttggaaacaag
+tgggagaggctgcctgatggcccgcaaagatttgacagctgtatcattgt
+tctgggctctccgagtttcctctctggccgccgttactgggaggtggagg
+ttggagacaagacagcatggatcctgggagcctgcaagacatccataagc
+aggaaagggaacatgactctgtcgccagagaatggctactgggtggtgat
+aatgatgaaggaaaatgagtaccaggcgtccagcgttcccccgacccgcc
+tgctaataaaggagcctcccaagcgtgtgggcatcttcgtggactacaga
+gttggaagcatctccttttacaatgtgacagccagatcccacatctatac
+attcgccagctgctctttctctgggccccttcaacctatcttcagccctg
+ggacacgtgatggagggaagaacacagctcctctgactatctgtccagtg
+ggtggtcaggggcctgactgaatgcccaacactgcatctctcttcctgct
+tctggccttgtatcttgcattcacactcaatagtcacggaatgccgac
+