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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lastz">Debian Med / lastz</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/lastz/-/commit/0a8e7e68b2031dbda4c65e4413b028da6c4de33a">0a8e7e68</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-15T13:31:01+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Propagate flags, Python3
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#d4eaf78ba7fd6549693a8523a6f0bc34d43581a2">
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debian/patches/propagate_cflags.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/lastz/-/commit/0a8e7e68b2031dbda4c65e4413b028da6c4de33a#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 15 Jun 2020 11:47:45 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: 2to3 for test suite</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/tools/any_to_qdna.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/any_to_qdna.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> """</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> Convert any file to a LASTZ quantum dna file, just by appending qdna headers</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -40,9 +40,9 @@</span> def usage(s=None):</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> def main():</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qdnaOldMagic = 0xF656659EL # big endian magic number for older qdna files</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qdnaMagic = 0xC4B47197L # big endian magic number for qdna files</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qdnaVersion = 0x00000200L </span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qdnaOldMagic = 0xF656659E # big endian magic number for older qdna files</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qdnaMagic = 0xC4B47197 # big endian magic number for qdna files</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qdnaVersion = 0x00000200 </span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> # parse args</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/axt_compare.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/axt_compare.py</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> Compare two axt files, reporting differences but ignoring some trivial ones</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> ---------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -56,11 +56,11 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> % (axt1Filename,axt2Filename)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if (different):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"FAILURE: %s" % message</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("FAILURE: %s" % message, file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"SUCCESS: %s and %s are equivalent" \</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (axt1Filename,axt2Filename)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("SUCCESS: %s and %s are equivalent" \</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (axt1Filename,axt2Filename), file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> # compare files</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/build_fasta_hsx.py</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/build_fasta_hsx.py</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> """</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> Build a "hashed sequence index" (hsx) file for a fasta file</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> -----------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -183,26 +183,26 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if (length == 0):</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> if (keepEmpties):</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "WARNING: keeping empty sequence %s (%s)" \</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (name,line_reference((fileName,lineNum)))</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("WARNING: keeping empty sequence %s (%s)" \</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (name,line_reference((fileName,lineNum))), file=sys.stderr)</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> else:</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "WARNING: discarding empty sequence %s (%s)" \</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (name,line_reference((fileName,lineNum)))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("WARNING: discarding empty sequence %s (%s)" \</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (name,line_reference((fileName,lineNum))), file=sys.stderr)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> continue</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> if (skipHeader): sequences += [(name,length,fileNum,seqOffset)]</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> else: sequences += [(name,length,fileNum,headerOffset)]</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> if ("progress" in debug) and (progress != None) and (seqNum % progress == 0):</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "read sequence %d (%s)" % (seqNum,name)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("read sequence %d (%s)" % (seqNum,name), file=sys.stderr)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> if (fileName != ""): f.close()</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> if ("progress" in debug):</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> if (fileName != ""):</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished reading %s" % fileName</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished reading %s" % fileName, file=sys.stderr)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> else:</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished reading input file"</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished reading input file", file=sys.stderr)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> # scan collected sequence info and assign hash values</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -218,12 +218,12 @@</span> def main():</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> sequences.sort()</span>
</pre>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> if ("progress" in debug):</span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished computing hashes"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished computing hashes", file=sys.stderr)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> if ("info" in debug):</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> for (hash,name,length,fileNum,offset) in sequences:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "%10d==%08X %2d:%08X %s %d" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (HsxFile.hash(name),hash,fileNum,offset,name,length)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%10d==%08X %2d:%08X %s %d" \</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (HsxFile.hash(name),hash,fileNum,offset,name,length), file=sys.stderr)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> ##########</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> # write the index</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="p">@@ -277,10 +277,10 @@</span> def main():</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> seqTableOffset = hashTableOffset + hashTableSize</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> if ("file" in debug):</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "fileTableOffset = %08X (%08X)" % (fileTableOffset,fileTableSize)</span></span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "fileInfoOffset = %08X (%08X)" % (fileInfoOffset,fileInfoSize)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "hashTableOffset = %08X (%08X)" % (hashTableOffset,hashTableSize)</span></span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "seqTableOffset = %08X" % seqTableOffset</span></span>
</pre>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("fileTableOffset = %08X (%08X)" % (fileTableOffset,fileTableSize), file=sys.stderr)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("fileInfoOffset = %08X (%08X)" % (fileInfoOffset,fileInfoSize), file=sys.stderr)</span></span>
</pre>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("hashTableOffset = %08X (%08X)" % (hashTableOffset,hashTableSize), file=sys.stderr)</span></span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("seqTableOffset = %08X" % seqTableOffset, file=sys.stderr)</span></span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> # determine offsets into the sequence table</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="p">@@ -313,7 +313,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> writeZeros(headerPad)</span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> if ("progress" in debug):</span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished writing header"</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished writing header", file=sys.stderr)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> # write file table and file info</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -329,7 +329,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> writeZeros(fileInfoPad)</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> if ("progress" in debug):</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished writing file table"</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished writing file table", file=sys.stderr)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> # write hash table</span>
</pre>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -346,14 +346,14 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> # output previous bucket</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> write5(seqOffset)</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> if ("progress" in debug) and (progress != None) and ((hash+1) % progress == 0):</span>
</pre>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "wrote hash bucket %d" % (hash+1)</span></span>
</pre>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("wrote hash bucket %d" % (hash+1), file=sys.stderr)</span></span>
</pre>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> # output intervening empty buckets</span>
</pre>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> prevHash += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> while (prevHash < hash):</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> write5(msBit5 + nameToOffset[name])</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> prevHash += 1</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> if ("progress" in debug) and (progress != None) and (prevHash % progress == 0):</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "wrote hash bucket %d" % (prevHash)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("wrote hash bucket %d" % (prevHash), file=sys.stderr)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> bucketSize = 1</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> seqOffset = nameToOffset[name]</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="p">@@ -373,7 +373,7 @@</span> def main():</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> writeZeros(hashTablePad)</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> if ("progress" in debug):</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished writing hash table"</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished writing hash table", file=sys.stderr)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> # write sequence table</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -383,10 +383,10 @@</span> def main():</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> write6(offset) # offset to the sequence data</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> writeString(name) # name of sequence</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> if ("progress" in debug) and (progress != None) and ((seqNum+1) % progress == 0):</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "wrote sequence entry %d" % (seqNum+1)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("wrote sequence entry %d" % (seqNum+1), file=sys.stderr)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> if ("progress" in debug):</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "finished writing index"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("finished writing index", file=sys.stderr)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> def pad_for_16(n):</span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="p">@@ -492,7 +492,8 @@</span> def sequence_name(s,nameParse=None):</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> else: return s.split()[0]</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def line_reference((fileName,lineNum)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def line_reference(xxx_todo_changeme):</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (fileName,lineNum) = xxx_todo_changeme</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> if (fileName == ""): return "line %d" % lineNum</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> else: return "line %s:%d" % (fileName,lineNum)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/expand_scores_file.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/expand_scores_file.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> Add scoring-related parameters to a lastz scores file</span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> -----------------------------------------------------</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -153,22 +153,22 @@</span> def main():</span>
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198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> blankLine = False</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> for ix in range(numValueLines):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print lines[ix]</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(lines[ix])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> blankLine = (lines[ix] == "")</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> if (addedNames != []):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (not blankLine): print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "# (score parameters added by expand_scores_file)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (not blankLine): print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("# (score parameters added by expand_scores_file)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> for name in addedNames:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s=%s" % (name,nameToVal[name])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s=%s" % (name,nameToVal[name]))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> blankLine = (lines[numValueLines] == "")</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (not blankLine): print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (not blankLine): print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> for ix in range(numValueLines,len(lines)):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
222
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print lines[ix]</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(lines[ix])</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> def int_or_float(s):</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/fasta_fragments.py</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/fasta_fragments.py</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> Break a fasta file into fragments.</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="p">@@ -82,13 +82,13 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> if (headLimit != None) and (fragNum > headLimit): break</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> seq = seq.upper()</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for ix in xrange(0,len(seq)-fragmentLength,stepLength):</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for ix in range(0,len(seq)-fragmentLength,stepLength):</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> frag = seq[ix:ix+fragmentLength]</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> if (frag == allN): continue</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> fragNum += 1</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> if (headLimit != None) and (fragNum > headLimit):</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>stderr, "limit of %d emitted fragments reached" % headLimit</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("limit of %d emitted fragments reached" % headLimit, file=stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> break</span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> if (origin == "zero"): header = ">%s_%d" % (name,ix)</span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="p">@@ -96,14 +96,14 @@</span> def main():</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> if (shuffleEm):</span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> fragments += [(header,frag)]</span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print header</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print frag</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(header)</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(frag)</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> if (shuffleEm):</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> shuffle(fragments)</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> for (header,frag) in fragments:</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print header</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print frag</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(header)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(frag)</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> # fasta_sequences--</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/fasta_softmask_intervals.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/fasta_softmask_intervals.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> """</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> Given a list of intervals, mask those bases in the fasta sequence(s).</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> """</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -130,12 +130,12 @@</span> def main():</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> prevEnd = end</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> if (prevEnd < len(seq)): newSeq += [seq[prevEnd:]]</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> </span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ">%s" % chrom</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(">%s" % chrom)</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> newSeq = "".join(newSeq)</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> assert (len(newSeq) == len(seq)), "internal error"</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> </span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> for i in range(0,len(newSeq),wrapLength):</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "".join(newSeq[i:i+wrapLength])</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("".join(newSeq[i:i+wrapLength]))</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> # make sure all sequences were given</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/gfa_compare.py</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/gfa_compare.py</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> Compare two gfa files, reporting differences but ignoring some trivial ones</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> ---------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="p">@@ -43,12 +43,12 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> else: (different,lineNum) = compare_sorted_files (gfa1,gfa2)</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> if (different):</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"FAILURE: %s and %s are different (line %d)" \</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (gfa1Filename,gfa2Filename,lineNum)</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("FAILURE: %s and %s are different (line %d)" \</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (gfa1Filename,gfa2Filename,lineNum), file=sys.stderr)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"SUCCESS: %s and %s are equivalent" \</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (gfa1Filename,gfa2Filename)</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("SUCCESS: %s and %s are equivalent" \</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (gfa1Filename,gfa2Filename), file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> # compare files that we expect are in the same order</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/hassock_hash.py</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/hassock_hash.py</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> Python implementation of the hash used for "hashed sequence index" files.</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> </span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="p">@@ -77,8 +77,8 @@</span> def main():</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> demonstrate_hash(line,m)</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> def demonstrate_hash(s,m):</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (m == None): print "%08X: %s" % (hassock_hash(s),s)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else: print "%d: %s" % (hassock_hash(s)%m,s)</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (m == None): print("%08X: %s" % (hassock_hash(s),s))</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else: print("%d: %s" % (hassock_hash(s)%m,s))</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> if __name__ == "__main__": main()</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/hsx_file.py</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/hsx_file.py</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> """</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> "Hashed sequence index" (hsx) file reader (for a fasta file)</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> -------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="p">@@ -87,9 +87,9 @@</span> class HsxFile(object):</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> else: self.debug = debug</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> self.open()</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> </span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- magicBig = 0xD2527095L</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- magicLittle = 0x957052D2L</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- version = 0x00000100L</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ magicBig = 0xD2527095</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ magicLittle = 0x957052D2</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ version = 0x00000100</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> msBit5 = 0x80 << (4*8)</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> </span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> def open(self):</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="p">@@ -168,22 +168,22 @@</span> class HsxFile(object):</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> def get_sequence(self,name):</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[fetching %s]" % name</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[fetching %s]" % name, file=sys.stderr)</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> # read hash bucket for this name</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> bucket = HsxFile.hash(name) % self.numBuckets</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ bucket = %d (file offset %08X)]" \</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (bucket,self.hashTableOffset+5*bucket)</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ bucket = %d (file offset %08X)]" \</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (bucket,self.hashTableOffset+5*bucket), file=sys.stderr)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> self.file.seek(self.hashTableOffset + 5*bucket)</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> bucketOffset = self.read5()</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> if (bucketOffset & HsxFile.msBit5 != 0):</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ bucket is empty]"</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ bucket is empty]", file=sys.stderr)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> return None</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> bucketEnd = self.read5() & ~HsxFile.msBit5</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ bucket offset = %010X..%010X ]" \</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (bucketOffset,bucketEnd)</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ bucket offset = %010X..%010X ]" \</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (bucketOffset,bucketEnd), file=sys.stderr)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> # scan the bucket until we find this sequence</span>
</pre>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> self.file.seek(bucketOffset)</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> seqIx = 1</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="p">@@ -194,15 +194,15 @@</span> class HsxFile(object):</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> seqOffset = self.read6()</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> seqName = self.readString()</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ (%010X) name %d = %s]" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (bucketOffset,seqIx,seqName)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ (%010X) name %d = %s]" \</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (bucketOffset,seqIx,seqName), file=sys.stderr)</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> if (seqName == name): break</span>
</pre>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> if (seqName > name): return None</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> bucketOffset += 1 + 6 + 5 + len(seqName) + 1</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> seqIx += 1</span>
</pre>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> if (seqName != name):</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ %s not in bucket]" % name</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ %s not in bucket]" % name, file=sys.stderr)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> return None</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> # open the sequence file (if it isn't already open)</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> assert (fileIx < len(self.fileTable)), \</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -211,12 +211,12 @@</span> class HsxFile(object):</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> (seqFileName,seqFile) = self.fileTable[fileIx]</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> if (seqFile == None):</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ opening %s]" % seqFileName</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ opening %s]" % seqFileName, file=sys.stderr)</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> seqFile = file(seqFileName,"rt")</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> self.fileTable[fileIx] = (seqFileName,seqFile)</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ reading from %s:%012X]" \</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (seqFileName,seqOffset)</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ reading from %s:%012X]" \</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (seqFileName,seqOffset), file=sys.stderr)</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> # read the sequence</span>
</pre>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> seqFile.seek(seqOffset)</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> seqLines = []</span>
</pre>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="p">@@ -226,7 +226,7 @@</span> class HsxFile(object):</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> if (line == ""): break</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> line = line.strip()</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> if ("fetch" in self.debug):</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "[ read %s]" % line</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ read %s]" % line, file=sys.stderr)</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> if (line.startswith(">")):</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> if (len(seqLines) != 0): break</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> seqLines += [line]</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/install_py.py</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/install_py.py</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="p">@@ -1,18 +1,18 @@</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> import string</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import commands</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> true = 1</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> false = 0</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> def do (command):</span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print command</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output = commands.getoutput(command)</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (len(output) > 0): print output</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(command)</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output = subprocess.getoutput(command)</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (len(output) > 0): print(output)</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> </span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> binDir = "~/py/bin"</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-currentDir = commands.getoutput("pwd").strip()</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+currentDir = subprocess.getoutput("pwd").strip()</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> args = sys.argv[1:]</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> remove = False</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/lav_compare.py</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/lav_compare.py</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> """</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> Compare two lav files, reporting differences but ignoring some trivial ones</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> ---------------------------------------------------------------------------</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="p">@@ -79,12 +79,12 @@</span> def main():</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> stanzaIx = 0</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> </span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> if (different):</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"FAILURE: %s and %s are different (line %d)" \</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (lav1Filename,lav2Filename,lineNum)</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("FAILURE: %s and %s are different (line %d)" \</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (lav1Filename,lav2Filename,lineNum), file=sys.stderr)</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> sys.exit(1)</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> </span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr,"SUCCESS: %s and %s are equivalent" \</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (lav1Filename,lav2Filename)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("SUCCESS: %s and %s are equivalent" \</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (lav1Filename,lav2Filename), file=sys.stderr)</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> </span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> </span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> def header_strip(s):</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/lav_sort.py</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/lav_sort.py</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> """</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> Sort the a-stanzas in a lav file, according to the user's choice of key</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> -----------------------------------------------------------------------</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="p">@@ -55,15 +55,15 @@</span> def main():</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> blocks.sort()</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> if (keyReverse): blocks.reverse()</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> for (key,s) in blocks:</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n".join(s)</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n".join(s))</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> blocks = []</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n".join(stanza)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n".join(stanza))</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> </span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> if (len(blocks) > 0):</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> blocks.sort()</span>
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<td class="diff-line-num new new_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> if (keyReverse): blocks.reverse()</span>
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<td class="diff-line-num new new_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> for (key,s) in blocks:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n".join(s)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n".join(s))</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> </span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> # read_stanzas--</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> # Collect the lines that belong to the next stanza. A stanza has the form</span>
</pre>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/maf_sort.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/maf_sort.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> Sort alignment blocks in a maf file, according to the user's choice of key</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> --------------------------------------------------------------------------</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="p">@@ -55,9 +55,9 @@</span> def main():</span>
</pre>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> if (keyReverse): blocks.reverse()</span>
</pre>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> for (key,block,comments) in blocks:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> if (comments != []):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n".join([line for line in comments])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n".join([line for line in block])</span></span>
</pre>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n".join([line for line in comments]))</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n".join([line for line in block]))</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> </span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> </span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> # read_blocks--</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/merge_masking_intervals.py</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge_masking_intervals.py</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> """</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> Given a file of masking intervals, combine overlapping intervals.</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> </span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="p">@@ -68,14 +68,14 @@</span> def main():</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"> if (start == None):</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> (start,end) = (s,e)</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> elif (s > end):</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%d\t%d" % (start+1,end)</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d\t%d" % (start+1,end))</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> (start,end) = (s,e)</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> continue</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> elif (e > end):</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> end = e</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> </span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> if (start != None):</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%d\t%d" % (start+1,end)</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d\t%d" % (start+1,end))</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> </span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> </span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> if __name__ == "__main__": main()</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/pick_from_fasta_hsx.py</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/pick_from_fasta_hsx.py</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> """</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> Select a subset of sequences from a fasta file indexed by an hsx file</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> ---------------------------------------------------------------------</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="p">@@ -75,11 +75,11 @@</span> def main():</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> for name in seqNames:</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> seq = hsx.get_sequence(name)</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> if (seq != None):</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print seq</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(seq)</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> if (showProgress):</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, name</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(name, file=sys.stderr)</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> elif (warnOnMissing):</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>sys.stderr, "WARNING: %s not found" % name</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("WARNING: %s not found" % name, file=sys.stderr)</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> hsx.close()</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> </span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> </span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/probabilities_to_scores.py</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/probabilities_to_scores.py</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> """</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> Convert probabilities to a LASTZ scores file (including quantum scores)</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> -----------------------------------------------------------------------</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="p">@@ -263,16 +263,16 @@</span> def main():</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> ##########</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> </span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> if ("debug" in debug):</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " ".join([" %s:%.5f" % (nuc,prob[nuc]) for nuc in bases])</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join([" %s:%.5f" % (nuc,prob[nuc]) for nuc in bases]))</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> </span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> for x in bases:</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " ".join(["%s:%.5f" % (x+y,prob[x+y]) for y in bases])</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(["%s:%.5f" % (x+y,prob[x+y]) for y in bases]))</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> </span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> for sym in symbols:</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> p = symProb[sym]</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s -> %s" \</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (sym," ".join([" %s:%.5f" % (nuc,p[nuc]) for nuc in bases]))</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s -> %s" \</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (sym," ".join([" %s:%.5f" % (nuc,p[nuc]) for nuc in bases])))</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> </span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> ##########</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> # write quantum code file</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="p">@@ -282,8 +282,8 @@</span> def main():</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> codeF = file(codeName,"wt")</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> for sym in symbols:</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> p = symProb[sym]</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >>codeF, "%s\t%s" \</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (sym,"\t".join(["%.6f" % p[nuc] for nuc in bases]))</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%s" \</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (sym,"\t".join(["%.6f" % p[nuc] for nuc in bases])), file=codeF)</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> codeF.close()</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> ##########</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="p">@@ -317,14 +317,14 @@</span> def main():</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> ##########</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> </span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> if (creator != None):</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "# created by %s" % creator</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("# created by %s" % creator)</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> </span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> if (settings != []):</span>
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<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> sLen = max([len(s) for (s,val) in settings])</span>
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<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> for (s,val) in settings:</span>
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<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s = %s" % (sLen,s,val)</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s = %s" % (sLen,s,val))</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> </span>
</pre>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> ##########</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> # print the substitution matrix</span>
</pre>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="p">@@ -336,17 +336,17 @@</span> def main():</span>
</pre>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> for col in colSymbols:</span>
</pre>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> wSub = max(wSub,len("%d" % sub[row][col]))</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> </span>
</pre>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s" \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols]))</span></span>
</pre>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s" \</span></span>
</pre>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols])))</span></span>
</pre>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s" \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (" "," ".join(["%*s" % (wSub,col) for col in colSymbols]))</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (" "," ".join(["%*s" % (wSub,col) for col in colSymbols])))</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> </span>
</pre>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> for row in rowSymbols:</span>
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<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s%s" \</span></span>
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655
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s%s" \</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> % (row,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> " ".join(["%*d" % (wSub,sub[row][col]) for col in colSymbols]),</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- non_single_comment(symGroup[row]))</span></span>
</pre>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ non_single_comment(symGroup[row])))</span></span>
</pre>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> </span>
</pre>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> else:</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> wSub = 4</span>
</pre>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="p">@@ -354,17 +354,17 @@</span> def main():</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> for col in colSymbols:</span>
</pre>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> wSub = max(wSub,len("%.6f" % sub[row][col]))</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> </span>
</pre>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s" \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols]))</span></span>
</pre>
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</tr>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s" \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols])))</span></span>
</pre>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s" \</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (" "," ".join(["%*s" % (wSub,col) for col in colSymbols]))</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s" \</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (" "," ".join(["%*s" % (wSub,col) for col in colSymbols])))</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> </span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> for row in rowSymbols:</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %s%s" \</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %s%s" \</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> % (row,</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> " ".join(["%*.6f" % (wSub,sub[row][col]) for col in colSymbols]),</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- non_single_comment(symGroup[row]))</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ non_single_comment(symGroup[row])))</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> def dna_event(s):</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/qcode_to_scores.py</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/qcode_to_scores.py</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> """</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> Convert quantum-code files to a LASTZ scores file</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> -------------------------------------------------</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="p">@@ -288,12 +288,12 @@</span> def main():</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> ##########</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> </span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"> if ("debug" in debug):</span>
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<td class="diff-line-num new new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "target" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- + " ".join([" %s:%.5f" % (nuc,rProb[nuc]) for nuc in bases])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "query" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- + " ".join([" %s:%.5f" % (nuc,cProb[nuc]) for nuc in bases])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("target" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + " ".join([" %s:%.5f" % (nuc,rProb[nuc]) for nuc in bases]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("query" \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + " ".join([" %s:%.5f" % (nuc,cProb[nuc]) for nuc in bases]))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> for y in bases:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
708
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " ".join(["%s:%.5f" % (y+x,rcProb[y+x]) for x in bases])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(["%s:%.5f" % (y+x,rcProb[y+x]) for x in bases]))</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> </span>
</pre>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> ##########</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> # assign scores</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="p">@@ -326,14 +326,14 @@</span> def main():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> ##########</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> if (creator != None):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
717
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "# created by %s" % creator</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("# created by %s" % creator)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> if (settings != []):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> sLen = max([len(s) for (s,val) in settings])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"> for (s,val) in settings:</span>
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<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s = %s" % (sLen,s,val)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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<td class="diff-line-num new new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s = %s" % (sLen,s,val))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> ##########</span>
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<td class="diff-line-num new new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> # print the substitution matrix</span>
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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="p">@@ -347,13 +347,13 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"> for col in colSymbols:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> wCol = max(wCol,len("%d" % sub[row][col]))</span>
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<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s %s" \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (wRow," "," ".join(["%*s" % (wCol,col) for col in colSymbols]))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s %s" \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (wRow," "," ".join(["%*s" % (wCol,col) for col in colSymbols])))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> for row in rowSymbols:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
742
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s %s" \</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s %s" \</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"> % (wRow,row,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- " ".join(["%*d" % (wCol,sub[row][col]) for col in colSymbols]))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ " ".join(["%*d" % (wCol,sub[row][col]) for col in colSymbols])))</span></span>
</pre>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> </span>
</pre>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> else:</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> wCol = 4</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="p">@@ -361,13 +361,13 @@</span> def main():</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"> for col in colSymbols:</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> wCol = max(wCol,len("%.6f" % sub[row][col]))</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"> </span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s %s" \</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- % (wRow," "," ".join(["%*s" % (wCol,col) for col in colSymbols]))</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s %s" \</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ % (wRow," "," ".join(["%*s" % (wCol,col) for col in colSymbols])))</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> </span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"> for row in rowSymbols:</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%-*s %s" \</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%-*s %s" \</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> % (wRow,row,</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- " ".join(["%*.6f" % (wCol,sub[row][col]) for col in colSymbols]))</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ " ".join(["%*.6f" % (wCol,sub[row][col]) for col in colSymbols])))</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"> </span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> </span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> def simple_dna_quantum_code():</span></pre>
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<li id="d4eaf78ba7fd6549693a8523a6f0bc34d43581a2">
<a href="https://salsa.debian.org/med-team/lastz/-/commit/0a8e7e68b2031dbda4c65e4413b028da6c4de33a#d4eaf78ba7fd6549693a8523a6f0bc34d43581a2"><strong>debian/patches/propagate_cflags.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 15 Jun 2020 11:47:45 +0200</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Propagate DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Also LDFLAGS is added to propagate remaining hardening options</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/src/Makefile</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -71,7 +71,7 @@</span> VERSION_FLAGS= \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> -DSUBVERSION_REV="\"${SUBVERSION_REV}"\"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS}</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -O3 ${definedForAll} ${VERSION_FLAGS}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> srcFiles = lastz infer_scores \</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -101,13 +101,13 @@</span> incFiles = lastz.h infer_scores.h \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> lastz: $(foreach part,${srcFiles},${part}.o)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} $(foreach part,${srcFiles},${part}.o) -lm -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} $(foreach part,${srcFiles},${part}.o) -lm -o $@ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> lastz_D: $(foreach part,${srcFiles},${part}_D.o)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} $(foreach part,${srcFiles},${part}_D.o) -lm -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} $(foreach part,${srcFiles},${part}_D.o) -lm -o $@ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> lastz_32: $(foreach part,${srcFiles},${part}_32.o)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} $(foreach part,${srcFiles},${part}_32.o) -lm -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} $(foreach part,${srcFiles},${part}_32.o) -lm -o $@ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # cleanup</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/0a8e7e68b2031dbda4c65e4413b028da6c4de33a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">propagate_cflags.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/0a8e7e68b2031dbda4c65e4413b028da6c4de33a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,18 +14,16 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_auto_test:</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> $(MAKE) base_tests</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> #$(MAKE) test</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> $(MAKE) clean_test</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">endif</span></pre>
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