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<h3>
Michael R. Crusoe pushed to branch simde
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7">641ad37a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-18T17:58:02Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">any-{amd64,i386}: multi-SIMD compile with dispatcher
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#1a0453e516e167132f0f9392c87de0ea5fe79145">
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+
debian/bin/simd-dispatch
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="1a0453e516e167132f0f9392c87de0ea5fe79145">
<a href="https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7#1a0453e516e167132f0f9392c87de0ea5fe79145"><strong>debian/bin/simd-dispatch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PKG</span><span class="o" style="font-weight: 600;">=</span>last-align</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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">DIR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASH_SOURCE</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">BASE</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">DIR</span><span class="k" style="font-weight: 600;">}</span>/../lib/<span class="nv" style="color: #008080;">$PKG</span>/<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>test_and_run <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> /proc/cpuinfo <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "${BASE}-$1" "$@"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></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="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SIMD <span class="k" style="font-weight: 600;">in </span>avx2 avx sse4.1 ssse3 sse3 sse2 sse mmx <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>test_and_run <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SIMD</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fallback to plain option</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">$BASE</span><span class="nt" style="color: #000080;">-plain</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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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">@@ -2,13 +2,9 @@ last-align (1021-3) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Enable building on any architecture via simde. (Closes: #946850)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * TODO</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> any-amd64: build multiple times with decreasing levels of</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -m{avx2,avx,sse4.1,ssse3,sse3,sse2}</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> any-i386: build multiple times with decreasing levels of</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -m{sse3,sse2,sse,mmx}</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> all of the above: add wrapper script to detect at runtime the highest</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> level of SIMD available, and launch the relevant binary</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * For any-amd64 and any-i386: compile multiple times with reducing levels of</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> SIMD instruction support and ship a dispatching script to pick the best</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> one for the user at run-time.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 16 Dec 2019 19:02:20 +0100</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</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">@@ -186,3 +186,90 @@</td>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="diff"> s2[-0][s1[0]]);</span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="diff"> SimdInt x = simdLoad(x2+i);</span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="diff"> SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="p">@@ -2,15 +2,24 @@</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> all:</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> </span>
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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"><span class="gd" style="color: #000; background-color: #fdd;">-progs = src/lastdb src/lastal src/last-split src/last-merge-batches \</span></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 class="gd" style="color: #000; background-color: #fdd;">-src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8</span></span>
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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="gi" style="color: #000; background-color: #dfd;">+SFX :=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+progs = src/lastdb$(SFX) src/lastal$(SFX) src/last-split$(SFX) \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/last-merge-batches$(SFX) src/last-pair-probs$(SFX) src/lastdb8$(SFX) \</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/lastal8$(SFX) src/last-split8$(SFX)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> </span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> prefix = /usr/local</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> exec_prefix = $(prefix)</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> bindir = $(exec_prefix)/bin</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libexecdir = $(exec_prefix)/libexec</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> install: all</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> mkdir -p $(bindir)</span>
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<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
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp $(progs) scripts/* $(bindir)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp scripts/* $(bindir)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifeq (,$(SFX))</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp $(progs) $(bindir)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp $(progs) $(libexecdir)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> @cd src && $(MAKE) clean</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- last-align.orig/src/makefile</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ last-align/src/makefile</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -56,8 +56,10 @@</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> </span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> MBOBJ = last-merge-batches.o</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> </span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ALL = lastdb lastal last-split last-merge-batches last-pair-probs \</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lastdb8 lastal8 last-split8</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SFX :=</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ALL = lastdb$(SFX) lastal$(SFX) last-split$(SFX) last-merge-batches$(SFX) \</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ last-pair-probs$(SFX) lastdb8$(SFX) lastal8$(SFX) last-split8$(SFX)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> indexObj8 = $(indexObj4:.o=.o8)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> alignObj8 = $(alignObj4:.o=.o8)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="p">@@ -66,33 +68,33 @@</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> all: $(ALL)</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> </span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> indexAllObj4 = $(indexObj0) $(indexObj4)</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lastdb: $(indexAllObj4)</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lastdb$(SFX): $(indexAllObj4)</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> indexAllObj8 = $(indexObj0) $(indexObj8)</span>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lastdb8: $(indexAllObj8)</span></span>
</pre>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lastdb8$(SFX): $(indexAllObj8)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz</span>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> alignAllObj4 = $(alignObj0) $(alignObj4)</span>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="248" 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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lastal: $(alignAllObj4)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lastal$(SFX): $(alignAllObj4)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="250" 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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz</span>
</pre>
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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>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> alignAllObj8 = $(alignObj0) $(alignObj8)</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"><span class="gd" style="color: #000; background-color: #fdd;">-lastal8: $(alignAllObj8)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lastal8$(SFX): $(alignAllObj8)</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz</span>
</pre>
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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>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="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"> splitAllObj4 = $(splitObj0) $(splitObj4)</span>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-last-split: $(splitAllObj4)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+last-split$(SFX): $(splitAllObj4)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> </span>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> splitAllObj8 = $(splitObj0) $(splitObj8)</span>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="263" 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">
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;">-last-split8: $(splitAllObj8)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+last-split8$(SFX): $(splitAllObj8)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="189" 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="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-last-pair-probs: $(PPOBJ)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+last-pair-probs$(SFX): $(PPOBJ)</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> </span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-last-merge-batches: $(MBOBJ)</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+last-merge-batches$(SFX): $(MBOBJ)</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> </span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> .SUFFIXES:</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,9 @@</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">mandir=$(prefix)/share/man/man1</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">libexecdir=$(prefix)/lib/$(DEB_SOURCE)</span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># Copy upstream CXXFLAGS here because makefile enables only overriding them</span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">CXXFLAGS += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3</span>
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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">@@ -18,18 +20,72 @@ CPPFLAGS += -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP</td>
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18
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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">LDFLAGS += -pthread</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">NUMJOBS = 1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> MAKEFLAGS += -j$(NUMJOBS)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">endif</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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21
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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22
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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23
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">%:</span>
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24
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> dh $@</span>
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25
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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26
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">override_dh_auto_build:</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> make all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> rm src/*.o? ; \</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> done</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 sse mmx; do \</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> rm src/*.o? ; \</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> done</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all SFX=-plain CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">else</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">endif</span>
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28
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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29
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">HELP2MAN = help2man --no-info --version-string="$(DEB_VERSION_UPSTREAM)"</span>
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30
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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31
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">override_dh_auto_install:</span>
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32
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<td class="diff-line-num new_line old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> make install prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) install SFX=-$${SIMD} prefix=$(prefix) libexecdir=$(libexecdir) ; \</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> done</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> mkdir -p $(prefix)/bin</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> cd $(prefix)/bin \</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 sse mmx plain; do \</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) install SFX=-$${SIMD} prefix=$(prefix) libexecdir=$(libexecdir) ; \</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> done</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> mkdir -p $(prefix)/bin</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> cd $(prefix)/bin \</span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">else</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> $(MAKE) -j$(NUMJOBS) install prefix=$(prefix)</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">endif</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">override_dh_auto_clean:</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> dh_auto_clean -- SFX=-$${SIMD} ; done</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 sse mmx plain; do \</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> dh_auto_clean -- SFX=-$${SIMD} ; done</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">else</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> dh_auto_clean</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">endif</span>
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33
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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34
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">override_dh_installman:</span>
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35
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> dh_installman</span>
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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">@@ -39,16 +95,16 @@ override_dh_installman:</td>
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39
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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40
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> --name="genome-scale comparison of biological sequences" \</span>
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41
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> --help-option="-h" \</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> $(<span class="idiff left right">CURDIR)/src</span>/lastal > $(mandir)/lastal.1</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> $(<span class="idiff left right">prefix)/bin</span>/lastal > $(mandir)/lastal.1</span>
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43
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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44
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> --name="genome-scale comparison of biological sequences" \</span>
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45
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> --help-option="-h" \</span>
</pre>
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46
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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> $(<span class="idiff left right">CURDIR)/src</span>/lastal8 > $(mandir)/lastal8.1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> $(<span class="idiff left right">prefix)/bin</span>/lastal8 > $(mandir)/lastal8.1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
47
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> # help2man output needs manual postprocessing - see debian/mans</span>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
48
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
49
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> # --name="genome-scale comparison of biological sequences" \</span>
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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
50
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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> # --help-option="-h" \</span>
</pre>
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51
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<td class="diff-line-num new_line old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> # $(<span class="idiff left right">CURDIR)/src</span>/lastdb > $(mandir)/lastdb.1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="52" 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="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> # $(<span class="idiff left right">prefix)/bin</span>/lastdb > $(mandir)/lastdb.1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> $(HELP2MAN) \</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
53
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> --name="Sort MAF-format alignments by sequence name" \</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
54
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> $(CURDIR)/scripts/maf-sort > $(mandir)/maf-sort.1</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,10 +128,10 @@ override_dh_installman:</td>
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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
72
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> # $(CURDIR)/scripts/last-remove-dominated > $(mandir)/last-remove-dominated.1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> $(HELP2MAN) \</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> --name='Estimates "split" or "spliced" alignments.' \</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<td class="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> $(<span class="idiff left right">CURDIR)/src</span>/last-split > $(mandir)/last-split.1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="76" 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="131" 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">
131
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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="LC131" class="line" lang="plaintext"> $(<span class="idiff left right">prefix)/bin</span>/last-split > $(mandir)/last-split.1</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"> $(HELP2MAN) \</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
77
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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"> --name='Estimates "split" or "spliced" alignments.' \</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> $(<span class="idiff left right">CURDIR)/src</span>/last-split8 > $(mandir)/last-split8.1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="79" 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="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> $(<span class="idiff left right">prefix)/bin</span>/last-split8 > $(mandir)/last-split8.1</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
79
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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> $(HELP2MAN) \</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
80
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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext"> --name="Join two or more sets of MAF-format multiple alignments" \</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
137
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> $(CURDIR)/scripts/maf-join > $(mandir)/maf-join.1</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,11 +143,11 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> $(CURDIR)/scripts/fastq-interleave > $(mandir)/fastq-interleave.1</span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext"> --name="Read files of lastal output, merge corresponding batches, and write them" \</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> $(<span class="idiff left right">CURDIR)/src</span>/last-merge-batches > $(mandir)/last-merge-batches.1</span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="plaintext"> $(<span class="idiff left right">prefix)/bin</span>/last-merge-batches > $(mandir)/last-merge-batches.1</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"> # help2man output needs manual postprocessing - see debian/mans</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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93
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> # --name="Read alignments of paired DNA reads to a genome, and do estimations" \</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> # $(<span class="idiff left right">CURDIR)/src</span>/last-pair-probs > $(mandir)/last-pair-probs.1</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> # $(<span class="idiff left right">prefix)/bin</span>/last-pair-probs > $(mandir)/last-pair-probs.1</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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96
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> $(CURDIR)/scripts/last-postmask > $(mandir)/last-postmask.1</span>
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