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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/af73543f5821c127550f2b1b023053e0f0636ef1">af73543f</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-05-17T18:15:35+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">i386: enable avx2, avx, and sse4.1 specific builds as well
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<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/bcc8c5f686990ac3beec20d80595b0168ce0d56c">bcc8c5f6</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-05-17T18:15:35+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Demote GNU parallel to a recommends; only used by parallel-fasta
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/830a97da55db70d0389a90a825c4b2c4d654f5bb...bcc8c5f686990ac3beec20d80595b0168ce0d56c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (1061-2) UNRELEASED; urgency=medium</span>
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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"> * i386: enable avx2, avx, and sse4.1 specific builds as well</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Demote GNU parallel to a recommends; only used by parallel-fasta</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 17 May 2020 12:32:51 +0200</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">last-align (1061-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/830a97da55db70d0389a90a825c4b2c4d654f5bb...bcc8c5f686990ac3beec20d80595b0168ce0d56c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -20,9 +20,9 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Built-Using: ${Built-Using}</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> parallel</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Recommends: python3,</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> python3-pil</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-pil,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> parallel</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: genome-scale comparison of biological sequences</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> LAST is software for comparing and aligning sequences, typically DNA or</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> protein sequences. LAST is similar to BLAST, but it copes better with very</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/830a97da55db70d0389a90a825c4b2c4d654f5bb...bcc8c5f686990ac3beec20d80595b0168ce0d56c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +40,7 @@ ifeq (amd64,$(DEB_HOST_ARCH))</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> for SIMD in <span class="idiff left right">ssse3 sse3 sse2 sse mmx</span>; do \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> for SIMD in <span class="idiff left right">avx2 avx sse4.1 ssse3 sse3 sse2 sse</span>; do \</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> dh_auto_build -- all SFX=-$${SIMD} ; \</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> find . -name '*.o' -delete ; \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,14 +79,14 @@ ifeq (amd64,$(DEB_HOST_ARCH))</td>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> dh_auto_clean -- SFX=-$${SIMD} ; done</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> for SIMD in <span class="idiff left right">ssse3 sse3 sse2 sse mmx</span> plain; do \</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> for SIMD in <span class="idiff left right">avx2 avx sse4.1 ssse3 sse3 sse2 sse</span> plain; do \</span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> dh_auto_clean -- SFX=-$${SIMD} ; done</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> for i in last-merge-batches last-pair-probs last-split last-split8 lastal lastal8 lastdb lastdb8; \</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> do \</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"> for j in avx avx2 sse2 sse3 sse4.1 ssse3 ; \</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> for j in avx avx2 sse2 sse3 sse4.1 ssse3 <span class="idiff left right">sse3 sse2 sse </span>; \</span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> do \</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> rm -f src/$$i-$$j ; \</span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> done ; \</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +105,7 @@ override_dh_installman:</td>
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105
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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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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> --help-option="-h" \</span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> $(prefix)/bin/lastal8 > $(mandir)/lastal8.1</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> # --name="genome-scale comparison of biological sequences" \</span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> # --help-option="-h" \</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" 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">@@ -116,7 +116,7 @@ override_dh_installman:</td>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> --name="changes the order of the sequences in MAF-format alignments" \</span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> $(CURDIR)/scripts/maf-swap > $(mandir)/maf-swap.1</span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> # --name="Add extra column with mapping probabilities" \</span>
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122
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> # $(CURDIR)/scripts/last-map-probs > $(mandir)/last-map-probs.1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -124,7 +124,7 @@ override_dh_installman:</td>
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124
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> # --name="Read files of lastal output, merge corresponding batches, and write them." \</span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> # $(CURDIR)/scripts/last-merge-batches > $(mandir)/last-merge-batches.1</span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"> # These scripts were droped</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"><span class="idiff left right"> # </span> # These scripts were droped</span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> # --name="Clean up MAF-format alignments" \</span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> # $(CURDIR)/scripts/last-reduce-alignments > $(mandir)/last-reduce-alignments.1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" 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="149" 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">@@ -149,7 +149,7 @@ override_dh_installman:</td>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> $(HELP2MAN) \</span>
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<td class="diff-line-num old_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> --name="Read files of lastal output, merge corresponding batches, and write them" \</span>
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<td class="diff-line-num old_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> $(prefix)/bin/last-merge-batches > $(mandir)/last-merge-batches.1</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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<td class="diff-line-num new old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"><span class="idiff left right"> </span># help2man output needs manual postprocessing - see debian/mans</span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> #$(HELP2MAN) \</span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> # --name="Read alignments of paired DNA reads to a genome, and do estimations" \</span>
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<td class="diff-line-num old_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> # $(prefix)/bin/last-pair-probs > $(mandir)/last-pair-probs.1</span>
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