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<h3>
Nilesh Patra pushed to branch upstream
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/d1b788bbe87c1e5812ec649f0952e53a399c2fc9">d1b788bb</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-01-28T17:19:22+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1178</pre>
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</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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</li>
<li class="file-stats">
<a href="#c86c7a6d9a7bc77f1c375315f47ff6952729ba5b">
doc/Makefile
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<li class="file-stats">
<a href="#2827a88da893d4d9713a74ea9ece8d5c14a78d93">
doc/last-evalues.html
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<li class="file-stats">
<a href="#15d31d5c4b02587fa590f72537ff73f2165bd0fb">
doc/last-evalues.txt
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<li class="file-stats">
<a href="#6589bbea45449d5b207f13f58d3f2b599925e199">
doc/last-papers.html
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<li class="file-stats">
<a href="#19ba723e869adc9a1e7514318f57c8664462ad22">
doc/last-papers.txt
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<li class="file-stats">
<a href="#ed50279e644d7f6c4780e3a19ddc00f6ef975a8b">
doc/last-postmask.html
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<li class="file-stats">
<a href="#8baea80cdbc459570d78b6db2030ec07c1dd0909">
doc/last-postmask.txt
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<li class="file-stats">
<a href="#4db689a65e7ef5a4449dcfaf14aed62c7a3556a1">
doc/last-split.html
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<li class="file-stats">
<a href="#5f5e686e75cf05fe83c2679635e96a5c9230bd0f">
doc/last-split.txt
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<li class="file-stats">
<a href="#bf068196d49b041029d9a269a6e3d52acda15f9f">
doc/last-train.html
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<li class="file-stats">
<a href="#03dd50d6a64beb7787e3bcc9eb6da79c482759d5">
doc/last-train.txt
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<li class="file-stats">
<a href="#095e933658235fc5dd1c9f7aa5ad547270953ccb">
doc/last-tuning.html
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<li class="file-stats">
<a href="#88b73917dd12cf720f9b24d29280ea7564d1e586">
doc/last-tuning.txt
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<li class="file-stats">
<a href="#650c803236dcc0d6e02c624b68d67f5be1a41d5e">
doc/last-tutorial.html
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<li class="file-stats">
<a href="#f9d530bbfca92a35437d8018b31c3726538723db">
doc/last-tutorial.txt
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<li class="file-stats">
<a href="#41cc9daec0be41234ba2e92831e904035b00c675">
doc/last.html
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<li class="file-stats">
<a href="#1eae4cca621ba67dde5fa0a501ceab79fa666725">
doc/last.txt
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<li class="file-stats">
<a href="#1d2db1d5c1263541e178e5c6d1a664dcaee43e97">
doc/lastal.html
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<li class="file-stats">
<a href="#30d864ed8925787ee70643db49814772753a5f2c">
doc/lastal.txt
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<li class="file-stats">
<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">
scripts/last-train
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<li class="file-stats">
<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
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<li class="file-stats">
<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">
src/LastalArguments.cc
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<li class="file-stats">
<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2021-01-27 Martin C. Frith <Martin C. Frith></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"> * doc/Makefile, doc/last-evalues.txt, doc/last-papers.txt, doc/last-</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> postmask.txt, doc/last-split.txt, doc/last-train.txt, doc/last-</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> tuning.txt, doc/last-tutorial.txt, doc/last.txt, doc/lastal.txt:</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> Big doc update</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ba6a55ed7287] [tip]</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">2021-01-25 Martin C. Frith <Martin C. Frith></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"> * doc/lastal.txt, scripts/last-train, src/LastalArguments.cc:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> train --codon: more data & better pseudocounts</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [9a6365d5825a]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">2021-01-14 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> * src/Alignment.cc, src/lastal.cc, test/last-test.out, test/last-</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Better repeat-masking for new-style frameshifts</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> [e8001aa6f633]</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">2021-01-13 Martin C. Frith <Martin C. Frith></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> [3713015a6ad3]</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> * src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> [69de4393c89c]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> * doc/last-papers.txt, src/lastal.cc:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> [2ad10ab5b4b1]</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">2021-01-05 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> * doc/last-train.txt, scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> last-train: add codon & frameshift options!</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> [977a35de8389]</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> * scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> Refactor</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> [663475110c85]</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">2020-12-28 Martin C. Frith <Martin C. Frith></span>
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2
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> * src/LastEvaluer.cc, src/mcf_frameshift_xdrop_aligner.cc,</span>
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4
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> src/mcf_frameshift_xdrop_aligner.hh, test/last-test.out:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> Fix E-values for new-style frameshifts</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [a55b81199602]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> [a55b81199602]</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">2020-12-23 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<li id="c86c7a6d9a7bc77f1c375315f47ff6952729ba5b">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#c86c7a6d9a7bc77f1c375315f47ff6952729ba5b"><strong>doc/Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,6 +13,8 @@ ${DOCS}: last-doc.css Makefile</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nl">.SUFFIXES</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">.html .txt</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">RST2HTML</span> <span class="o" style="font-weight: 600;">=</span> rst2html <span class="c" style="color: #998; font-style: italic;"># xxx .py ???</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Ugh! Is there a better way?</span></span>
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<td class="diff-line-num new_line" data-linenumber="19" 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nv" style="color: #008080;">RST_CSS</span> <span class="o" style="font-weight: 600;">=</span> <span class="sb" style="color: #d14;">`</span>locate html4css1.css | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#RST_CSS = html4css1.css</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="23" 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">@@ -21,7 +23,7 @@ RSTFLAGS = --initial-header-level=2 --no-compact-lists \</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="nt" style="color: #000080;">--no-compact-field-lists</span> <span class="nt" style="color: #000080;">--option-limit</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: #000080;">--no-doc-info</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nl">.txt.html</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="idiff left right">rst2html</span> <span class="nt" style="color: #000080;">--stylesheet-path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">${RST_CSS}</span>,last-doc.css <span class="nv" style="color: #008080;">${RSTFLAGS}</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left right">${RST2HTML}</span></span> <span class="nt" style="color: #000080;">--stylesheet-path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">${RST_CSS}</span>,last-doc.css <span class="nv" style="color: #008080;">${RSTFLAGS}</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="nl">last-matrices.txt</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">../data/*.mat</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> ../build/mat-doc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></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">@@ -367,9 +367,6 @@ option -v (verbose).</p></td>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If your sequences have very different letter frequencies (e.g. very</span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="html">AT-rich DNA), the E-values will be misleading. The best solution is</span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="html">to use a suitable score matrix, such as AT77 or ATMAP.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For DNA-versus-protein alignment, however, only the protein</span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="html">frequencies are determined by the score matrix. The DNA frequencies</span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="html">are fixed at 0.25.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"calculation-of-eg2"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Calculation of EG2<span class="nt" style="color: #000080;"></h3></span></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">@@ -426,12 +423,12 @@ or gap costs (e.g. match score = 99, mismatch cost = 1). In such</td>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="html">cases, lastal requires you to set a score threshold with option -e.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>There may be a long startup time to calculate the E-value parameters</span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="html">(lambda, K, and finite-size correction parameters)<span class="idiff left right">, especially for</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="html">a<span class="idiff left right">lignment with frameshifts. This is avoided, for particular scoring</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="html"><span class="idiff left right">schemes, by storing the parameters in LAST's source code.</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="html"><span class="idiff left right">Parameters for other scoring schemes can be added on request. (Or</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="html"><span class="idiff left right">you can do it yourself: run lastal with option -v, so it prints the</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="html"><span class="idiff left right">E-value parameters, then copy them into </span>LastEvaluer.cc.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="html">(lambda, K, and finite-size correction parameters)<span class="idiff left right">. This is</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="html">a<span class="idiff left right">voided, for particular scoring schemes, by storing the parameters</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="html"><span class="idiff left right">in LAST's source code. Parameters for other scoring schemes can be</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="html"><span class="idiff left right">added on request. (Or you can do it yourself: run lastal with</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="html"><span class="idiff left right">option -v, so it prints the E-value parameters, then copy them into</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="html">LastEvaluer.cc.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>The E-values do not account for lastal option -c. If you use this</span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="html">option, the E-values will be under-estimates.<span class="nt" style="color: #000080;"></p></span></span>
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<li id="15d31d5c4b02587fa590f72537ff73f2165bd0fb">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#15d31d5c4b02587fa590f72537ff73f2165bd0fb"><strong>doc/last-evalues.txt</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">@@ -58,10 +58,6 @@ If your sequences have very different letter frequencies (e.g. very</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">AT-rich DNA), the E-values will be misleading. The best solution is</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">to use a suitable score matrix, such as AT77 or ATMAP.</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">For DNA-versus-protein alignment, however, only the protein</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">frequencies are determined by the score matrix. The DNA frequencies</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">are fixed at 0.25.</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">Calculation of EG2</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></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">@@ -115,12 +111,12 @@ Limitations</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> cases, lastal requires you to set a score threshold with option -e.</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">* There may be a long startup time to calculate the E-value parameters</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> (lambda, K, and finite-size correction parameters)<span class="idiff left right">, especially for</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> a<span class="idiff left right">lignment with frameshifts. This is avoided, for particular scoring</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> <span class="idiff left right">schemes, by storing the parameters in LAST's source code.</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> <span class="idiff left right">Parameters for other scoring schemes can be added on request. (Or</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> <span class="idiff left right">you can do it yourself: run lastal with option -v, so it prints the</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> <span class="idiff left right">E-value parameters, then copy them into </span>LastEvaluer.cc.)</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> (lambda, K, and finite-size correction parameters)<span class="idiff left right">. This is</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> a<span class="idiff left right">voided, for particular scoring schemes, by storing the parameters</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> <span class="idiff left right">in LAST's source code. Parameters for other scoring schemes can be</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> <span class="idiff left right">added on request. (Or you can do it yourself: run lastal with</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> <span class="idiff left right">option -v, so it prints the E-value parameters, then copy them into</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> LastEvaluer.cc.)</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">* The E-values do not account for lastal option -c. If you use this</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> option, the E-values will be under-estimates.</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">@@ -377,7 +377,8 @@ Res. 2014 42(7):e59.</p></td>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bioinformatics.oxfordjournals.org/content/30/24/3575.long"</span><span class="nt" style="color: #000080;">></span>Frameshift alignment: statistics and post-genomic</span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="html">applications<span class="nt" style="color: #000080;"></a></span>. Sheetlin SL, Park Y, Frith MC, Spouge JL.</span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="html">Bioinformatics. 2014 30(24):3575-82.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes DNA-versus-protein alignment allowing for frameshifts.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes <span class="ni" style="color: #800080;">"</span>old-style<span class="ni" style="color: #800080;">"</span> DNA-versus-protein alignment allowing for</span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="html">frameshifts (without <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></span></tt></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://www.genomebiology.com/content/16/1/106"</span><span class="nt" style="color: #000080;">></span>Split-alignment of genomes finds orthologies more accurately<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="html">Frith MC, Kawaguchi R. Genome Biology. 2015 16:106.<span class="nt" style="color: #000080;"></p></span></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">@@ -387,13 +388,22 @@ whole genome alignment.</p></td>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw742"</span><span class="nt" style="color: #000080;">></span>Training alignment parameters for arbitrary sequencers with</span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="html">LAST-TRAIN<span class="nt" style="color: #000080;"></a></span>. Hamada M, Ono Y, Asai K Frith MC.</span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="html">Bioinformatics. 2017 33(6):926-928.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes <span class="idiff left right">last-train</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">last-train</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://ieeexplore.ieee.org/document/8288582/"</span><span class="nt" style="color: #000080;">></span>A Simplified Description of Child Tables for Sequence Similarity</span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="html">Search<span class="nt" style="color: #000080;"></a></span>. Frith MC, Shrestha A. IEEE/ACM Trans Comput Biol</span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="html">Bioinform. 2018.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes how LAST uses child tables.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/bioinformatics/btaa1054"</span><span class="nt" style="color: #000080;">></span>Minimally-overlapping words for sequence similarity search<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="html">Frith MC, Noé L, Kucherov G. Bioinformatics. 2020<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes the <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>lastdb <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-u<span class="nt" style="color: #000080;"></span></span> RY<span class="nt" style="color: #000080;"></tt></span> sparsity options.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1101/2021.01.25.428050"</span><span class="nt" style="color: #000080;">></span>Improved DNA-versus-protein homology search for protein fossils<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="html">Yao Y, Frith MC.<span class="nt" style="color: #000080;"></p></span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Describes <span class="ni" style="color: #800080;">"</span>new-style<span class="ni" style="color: #800080;">"</span> DNA-versus-protein search with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></span></span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html"><span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"external-methods"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>External methods<span class="nt" style="color: #000080;"></h2></span></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">@@ -90,7 +90,8 @@ research to society.</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> __ http://bioinformatics.oxfordjournals.org/content/30/24/3575.long</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> Describes DNA-versus-protein alignment allowing for frameshifts.</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> Describes "old-style" DNA-versus-protein alignment allowing for</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> frameshifts (without ``last-train``).</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">11. `Split-alignment of genomes finds orthologies more accurately`__.</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> Frith MC, Kawaguchi R. Genome Biology. 2015 16:106.</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">@@ -106,7 +107,7 @@ research to society.</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> __ https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw742</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> Describes <span class="idiff left right">last-train</span>.</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> Describes <span class="idiff left right">``last-train``</span>.</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">13. `A Simplified Description of Child Tables for Sequence Similarity</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> Search`__. Frith MC, Shrestha A. IEEE/ACM Trans Comput Biol</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">@@ -116,6 +117,21 @@ research to society.</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> Describes how LAST uses child tables.</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">14. `Minimally-overlapping words for sequence similarity search`__.</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> Frith MC, Noé L, Kucherov G. Bioinformatics. 2020</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> __ https://doi.org/10.1093/bioinformatics/btaa1054</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> Describes the ``lastdb -u RY`` sparsity options.</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">15. `Improved DNA-versus-protein homology search for protein fossils`__.</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> Yao Y, Frith MC.</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> __ https://doi.org/10.1101/2021.01.25.428050</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> Describes "new-style" DNA-versus-protein search with ``last-train</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> --codon``.</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext">External methods</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">----------------</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">@@ -319,9 +319,9 @@ table.field-list { border: thin solid green }</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>last-postmask<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This script does post-alignment masking. It reads pair-wise sequence</span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html">alignments, and <span class="idiff left right">writes only those that align a significant amount of</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html"><span class="idiff left right">uppercase sequence. (Lowercase is often used to indicate undesirable</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="html"><span class="idiff left right">repetitive regions</span>.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="html">alignments, and <span class="idiff left right">only writes alignments that include a significant</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="html"><span class="idiff left right">amount of uppercase-to-uppercase alignment. (Lowercase is often used</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="html"><span class="idiff left">to indicate undesirable </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">simple</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> sequence</span>.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The input should be in MAF format, with header lines (of the kind</span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="html">produced by lastal) describing the alignment score parameters.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The script discards alignments that lack any segment with score <span class="ni" style="color: #800080;">></span>=</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">@@ -2,9 +2,9 @@ last-postmask</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"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">This script does post-alignment masking. It reads pair-wise sequence</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">alignments, and <span class="idiff left right">writes only those that align a significant amount of</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">uppercase sequence. (Lowercase is often used to indicate undesirable</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">repetitive regions</span>.)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">alignments, and <span class="idiff left right">only writes alignments that include a significant</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">amount of uppercase-to-uppercase alignment. (Lowercase is often used</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">to indicate undesirable "simple" sequence</span>.)</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">The input should be in MAF format, with header lines (of the kind</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">produced by lastal) describing the alignment score parameters.</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">@@ -364,7 +364,7 @@ last-split options.</p></td>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"alignment-of-two-whole-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Alignment of two whole genomes<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"<span class="idiff left right">https://github.com/mcfrith/last-genome-alignments</span>"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"<span class="idiff left right">last-tutorial.html</span>"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"faq"</span><span class="nt" style="color: #000080;">></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#5f5e686e75cf05fe83c2679635e96a5c9230bd0f"><strong>doc/last-split.txt</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">@@ -54,7 +54,7 @@ last-split options.</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">Alignment of two whole genomes</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">See `here <<span class="idiff left right">https://github.com/mcfrith/last-genome-alignments</span>>`_.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">See `here <<span class="idiff left right">last-tutorial.html</span>>`_.</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">FAQ</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">---</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">@@ -399,6 +399,13 @@ include 2 for half-bit scores and 3 for 1/3-bit scores.</td>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="html">(Note that 1/3-bit scores essentially equal Phred scores</span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="html">a.k.a. decibans, because log10(2) ≈ 3/10.) The default is to</span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="html">infer a scale from the initial score parameters.<span class="nt" style="color: #000080;"></td></tr></span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></kbd></td></span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Do training for DNA query sequences versus protein reference</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html">sequences. These options will be ignored: <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--revsym<span class="nt" style="color: #000080;"></span></span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="html"><span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--matsym<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--gapsym<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--pid<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--postmask<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-q<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-p<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-S<span class="nt" style="color: #000080;"></span></tt></span>. If</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></tt></span> is used, the <span class="ni" style="color: #800080;">"</span>initial parameter options<span class="ni" style="color: #800080;">"</span> are</span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="html">initial probabilities, not scores/costs.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="html"><span class="nt" style="color: #000080;"></tbody></span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="html"><span class="nt" style="color: #000080;"></table></span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></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">@@ -433,6 +440,9 @@ alignments: they are described in more detail at <a class="reference external" h</td>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-B <span class="nt" style="color: #000080;"><var></span>COST<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Initial insertion extension cost.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-F <span class="nt" style="color: #000080;"><var></span>LIST<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Initial frameshift probabilities (only used with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></tt></span>).<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="html"><span class="nt" style="color: #000080;"></tbody></span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></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">@@ -557,10 +567,7 @@ may be poor.</p></td>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>last-train can fail for various reasons, e.g. if the sequences are</span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="html">too dissimilar. If it fails to find any alignments, you could try</span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-tutorial.html#example-6-find-very-short-dna-alignments"</span><span class="nt" style="color: #000080;">></span>reducing the alignment significance threshold<span class="nt" style="color: #000080;"></a></span> with</span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="html">option -D.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>last-train cannot handle DNA-versus-protein alignment.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="html">reducing the alignment <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significance<span class="nt" style="color: #000080;"></a></span> threshold with option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-D<span class="nt" style="color: #000080;"></span></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#03dd50d6a64beb7787e3bcc9eb6da79c482759d5"><strong>doc/last-train.txt</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">@@ -65,6 +65,12 @@ Training options</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> (Note that 1/3-bit scores essentially equal Phred scores</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> a.k.a. decibans, because log10(2) ≈ 3/10.) The default is to</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> infer a scale from the initial score parameters.</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> --codon</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> Do training for DNA query sequences versus protein reference</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> sequences. These options will be ignored: ``--revsym</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> --matsym --gapsym --pid --postmask -q -p -S``. If</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> ``--codon`` is used, the "initial parameter options" are</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> initial probabilities, not scores/costs.</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">All options below this point are passed to lastal to do the</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">alignments: they are described in more detail at `<lastal.html>`_.</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">@@ -79,6 +85,7 @@ Initial parameter options</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> -b COST Initial gap extension cost.</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> -A COST Initial insertion existence cost.</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> -B COST Initial insertion extension cost.</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> -F LIST Initial frameshift probabilities (only used with ``--codon``).</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">Alignment options</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~</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">@@ -174,8 +181,6 @@ Bugs</td>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">* last-train can fail for various reasons, e.g. if the sequences are</span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"> too dissimilar. If it fails to find any alignments, you could try</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"> `reducing the alignment significance threshold</span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> <last-tutorial.html#example-6-find-very-short-dna-alignments>`_ with</span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"> option -D.</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> reducing the alignment significance_ threshold with option ``-D``.</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"><span class="idiff left right">* last-train cannot handle DNA-versus-protein alignment.</span></span></pre>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"><span class="idiff left right">.. _significance: last-evalues.html</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#095e933658235fc5dd1c9f7aa5ad547270953ccb"><strong>doc/last-tuning.html</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">@@ -320,13 +320,6 @@ table.field-list { border: thin solid green }</td>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This document tells you how to trade-off <span class="nt" style="color: #000080;"><strong></span>speed<span class="nt" style="color: #000080;"></strong></span>, <span class="nt" style="color: #000080;"><strong></span>sensitivity<span class="nt" style="color: #000080;"></strong></span>,</span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="html">and <span class="nt" style="color: #000080;"><strong></span>memory and disk usage<span class="nt" style="color: #000080;"></strong></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Ideally, the default settings would always work well. Unfortunately,</span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="html">there is too great a variety of challenging alignment tasks, and the</span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html">LAST developers lack experience with most of them.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST must have <span class="nt" style="color: #000080;"><em></span>some<span class="nt" style="color: #000080;"></em></span> defaults, and any choice will displease someone.</span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="html">It is wrong to say <span class="ni" style="color: #800080;">"</span>LAST is faster but less sensitive than method X<span class="ni" style="color: #800080;">"</span>,</span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="html">or <span class="ni" style="color: #800080;">"</span>slower but more sensitive than method Y<span class="ni" style="color: #800080;">"</span>, without varying the</span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html">defaults.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"sparsity-options"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Sparsity options<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>It's advisable to use at most one sparsity option: combining them will</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">@@ -409,7 +402,7 @@ high-identity matches.</p></td>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastal -C<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This option (gapless alignment culling) can make lastal <span class="nt" style="color: #000080;"><strong></span>faster<span class="nt" style="color: #000080;"></strong></span> but</span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"><strong></span>less sensitive<span class="nt" style="color: #000080;"></strong></span>. It can also <span class="nt" style="color: #000080;"><strong></span>reduce redundant output<span class="nt" style="color: #000080;"></strong></span>. For</span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="html">example, <span class="idiff left right">-C2</span> makes it discard alignments (before gapped extension)</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html">example, <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-C2</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> makes it discard alignments (before gapped extension)</span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="html">whose query coordinates lie in those of 2 or more stronger alignments.</span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html">This works well for aligning long, repeat-rich, indel-poor sequences</span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="html">(e.g. mammal chromosomes) without repeat-masking.<span class="nt" style="color: #000080;"></p></span></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">@@ -421,13 +414,13 @@ sets the maximum score drop in alignments, in the gapped extension</td>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="html">phase. Lower values make it faster, by quitting unpromising</span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="html">extensions sooner. The default aims at best accuracy.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You can set this option in several ways: perhaps the most intuitive is</span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="html">via maximum gap length. For example, <span class="idiff left right">-z10g</span> sets the maximum score</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="html">via maximum gap length. For example, <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-z10g</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> sets the maximum score</span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="html">drop such that the longest possible gap length is 10.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"lastal-x"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastal -x<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This option (preliminary gapped extension) can make lastal <span class="nt" style="color: #000080;"><strong></span>faster<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="html">but <span class="nt" style="color: #000080;"><strong></span>less sensitive<span class="nt" style="color: #000080;"></strong></span>. For example, <span class="idiff left right">-x2g</span> makes it extend gapped</span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="html">but <span class="nt" style="color: #000080;"><strong></span>less sensitive<span class="nt" style="color: #000080;"></strong></span>. For example, <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-x2g</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> makes it extend gapped</span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="html">alignments with a maximum gap length of 2, discard those with score</span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="html">below the gapped score threshold, then redo the survivors with the</span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="html">final max score drop (z).<span class="nt" style="color: #000080;"></p></span></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">@@ -442,17 +435,17 @@ gaps).</p></td>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"lastal-j1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastal -j1<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This option requests <span class="nt" style="color: #000080;"><strong></span>gapless<span class="nt" style="color: #000080;"></strong></span> alignment, which is even <span class="nt" style="color: #000080;"><strong></span>faster<span class="nt" style="color: #000080;"></strong></span>.</span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="html">(You could get the same effect by using very high gap costs, but<span class="idiff left right"> -j1</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="html">is faster because it skips the gapping phase entirely.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="html">(You could get the same effect by using very high gap costs, but</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-j1</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right"> </span>is faster because it skips the gapping phase entirely.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"lastal-f"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastal -f<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Option <span class="idiff left right">-fTAB</span> <span class="nt" style="color: #000080;"><strong></span>reduces the output size<span class="nt" style="color: #000080;"></strong></span>, which can improve speed.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Option <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-fTAB</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> <span class="nt" style="color: #000080;"><strong></span>reduces the output size<span class="nt" style="color: #000080;"></strong></span>, which can improve speed.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"lastdb-i"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastdb -i<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This option <span class="nt" style="color: #000080;"><strong></span>makes lastdb faster<span class="nt" style="color: #000080;"></strong></span>, but disables some lastal options.</span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="html">If lastdb is too slow, try <span class="idiff left right">-i10</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="html">If lastdb is too slow, try <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-i10</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"lastdb-c2"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>lastdb -C2<span class="nt" style="color: #000080;"></h3></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#88b73917dd12cf720f9b24d29280ea7564d1e586"><strong>doc/last-tuning.txt</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">@@ -4,15 +4,6 @@ LAST Performance Tuning</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">This document tells you how to trade-off **speed**, **sensitivity**,</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">and **memory and disk usage**.</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">Ideally, the default settings would always work well. Unfortunately,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">there is too great a variety of challenging alignment tasks, and the</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">LAST developers lack experience with most of them.</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">LAST must have *some* defaults, and any choice will displease someone.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">It is wrong to say "LAST is faster but less sensitive than method X",</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">or "slower but more sensitive than method Y", without varying the</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">defaults.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Sparsity options</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"></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">@@ -110,7 +101,7 @@ lastal -C</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">This option (gapless alignment culling) can make lastal **faster** but</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">**less sensitive**. It can also **reduce redundant output**. For</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">example, <span class="idiff left right">-C2</span> makes it discard alignments (before gapped extension)</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">example, <span class="idiff left right">``-C2``</span> makes it discard alignments (before gapped extension)</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">whose query coordinates lie in those of 2 or more stronger alignments.</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">This works well for aligning long, repeat-rich, indel-poor sequences</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">(e.g. mammal chromosomes) without repeat-masking.</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">@@ -124,14 +115,14 @@ phase. Lower values make it faster, by quitting unpromising</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">extensions sooner. The default aims at best accuracy.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">You can set this option in several ways: perhaps the most intuitive is</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">via maximum gap length. For example, <span class="idiff left right">-z10g</span> sets the maximum score</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">via maximum gap length. For example, <span class="idiff left right">``-z10g``</span> sets the maximum score</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">drop such that the longest possible gap length is 10.</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">lastal -x</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">---------</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext">This option (preliminary gapped extension) can make lastal **faster**</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">but **less sensitive**. For example, <span class="idiff left right">-x2g</span> makes it extend gapped</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">but **less sensitive**. For example, <span class="idiff left right">``-x2g``</span> makes it extend gapped</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">alignments with a maximum gap length of 2, discard those with score</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">below the gapped score threshold, then redo the survivors with the</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext">final max score drop (z).</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">@@ -148,19 +139,19 @@ lastal -j1</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">----------</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">This option requests **gapless** alignment, which is even **faster**.</span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext">(You could get the same effect by using very high gap costs, but<span class="idiff left right"> -j1</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">is faster because it skips the gapping phase entirely.)</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">(You could get the same effect by using very high gap costs, but</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"><span class="idiff left right">``-j1`` </span>is faster because it skips the gapping phase entirely.)</span>
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153
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"></span>
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154
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext">lastal -f</span>
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155
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">---------</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext">Option <span class="idiff left right">-fTAB</span> **reduces the output size**, which can improve speed.</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">Option <span class="idiff left right">``-fTAB``</span> **reduces the output size**, which can improve speed.</span>
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158
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">lastdb -i</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">---------</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">This option **makes lastdb faster**, but disables some lastal options.</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">If lastdb is too slow, try <span class="idiff left right">-i10</span>.</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">If lastdb is too slow, try <span class="idiff left right">``-i10``</span>.</span>
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164
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext">lastdb -C2</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">----------</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><title></span>LAST <span class="idiff left right">Tutorial</span><span class="nt" style="color: #000080;"></title></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><title></span>LAST <span class="idiff left right">Cookbook</span><span class="nt" style="color: #000080;"></title></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">/*</span></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">@@ -315,206 +315,306 @@ table.field-list { border: thin solid green }</td>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"document"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"last-tutorial"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>LAST Tutorial<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST finds similar regions between sequences, and aligns them.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-1-compare-the-human-and-fugu-mitochondrial-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 1: Compare the human and fugu mitochondrial genomes<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For our first example, we wish to find and align similar regions</span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html">between the human and fugu mitochondrial genomes. You can find these</span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="html">sequences in the examples directory: humanMito.fa and fuguMito.fa. We</span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="html">can compare them like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"document"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"last-cookbook"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>LAST Cookbook<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last.html"</span><span class="nt" style="color: #000080;">></span>LAST<span class="nt" style="color: #000080;"></a></span> is used by running commands in a terminal / command line. It</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="html">has many options: unfortunately, the LAST developers don't know the</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="html">best options for every possible alignment task. Here are some</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="html">reasonable starting points. Feel free to optimize (and share!) search</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="html">protocols.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"a-minimal-example-compare-human-fugu-mitochondrial-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>A minimal example: compare human <span class="ni" style="color: #800080;">&</span> fugu mitochondrial genomes<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Let's find and align similar regions between the human and fugu</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="html">mitochondrial genomes. These FASTA-format files are in LAST's</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="html">examples directory: humanMito.fa and fuguMito.fa. The simplest</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="html">possible usage is:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html">lastdb <span class="idiff left right">-cR01 </span>humdb humanMito.fa</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="html">lastdb humdb humanMito.fa</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="html">lastal humdb fuguMito.fa <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="idiff left right">lastdb</span> command creates several files whose names begin with</span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="html"><span class="ni" style="color: #800080;">"</span>humdb<span class="ni" style="color: #800080;">"</span>. The <span class="idiff left right">lastal</span> command then compares fuguMito.fa to the humdb</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="nt" style="color: #000080;"><span class="idiff left"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"lastdb.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">lastdb</span><span class="nt" style="color: #000080;"><span class="idiff right"></a></span></span> command creates several files whose names begin with</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="html"><span class="ni" style="color: #800080;">"</span>humdb<span class="ni" style="color: #800080;">"</span>. The <span class="nt" style="color: #000080;"><span class="idiff left"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"lastal.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">lastal</span><span class="nt" style="color: #000080;"><span class="idiff right"></a></span></span> command then compares fuguMito.fa to the humdb</span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="html">files, and writes the alignments to a file called <span class="ni" style="color: #800080;">"</span>myalns.maf<span class="ni" style="color: #800080;">"</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="ni" style="color: #800080;">"</span>-cR01<span class="ni" style="color: #800080;">"</span> option suppresses alignments caused by simple sequence</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="html">such as cacacacacacacacacacacaca.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"understanding-the-output"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Understanding the output<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The output has very long lines, so you need to view it without</span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="html">line-wrapping. For example, with a Unix/Linux/MacOsX command line,</span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="html">you can use:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="html">line-wrapping. For example, you can use:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="html">less -S myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Each alignment looks like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Each alignment looks like this<span class="idiff left"> (</span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"http://genome.ucsc.edu/FAQ/FAQformat.html#format5"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">MAF</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff right"> format)</span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="html">a score=27 EG2=4.7e+04 E=2.6e-05</span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="html">s humanMito 2170 145 + 16571 AGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTT...</span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="html">s fuguMito 1648 142 + 16447 AGTAGGCTTAGAAGCAGCCACCA--CAAGAAAGCGTT...</span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The score is a measure of how significant the similarity is. EG2 and</span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="html">E are explained at <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>last-evalues<span class="idiff left">.html</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff">. Lines starting with </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">s</span><span class="ni" style="color: #800080;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="html"><span class="idiff left right">contain: the sequence name, the start coordinate of the alignment, the</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="html"><span class="idiff left right">number of bases spanned by the alignment, the strand, the sequence</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="html"><span class="idiff left right">length, </span>and the aligned bases.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="html">E are explained at <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>last-evalues<span class="nt" style="color: #000080;"><span class="idiff left"></a></span></span><span class="idiff">. Lines starting with </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">s</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> contain:</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="html"><span class="idiff left right">the sequence name, the start coordinate of the alignment, the number</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html"><span class="idiff left right">of bases spanned by the alignment, the strand, the sequence length,</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html">and the aligned bases.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The start coordinates are zero-based. This means that, if the</span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="html">alignment begins right at the start of a sequence, the coordinate is</span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="html">0. If the strand is <span class="ni" style="color: #800080;">"</span>-<span class="ni" style="color: #800080;">"</span>, the start coordinate is <span class="idiff left right">in the reverse</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="html"><span class="idiff left">strand.</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span><span class="idiff">This alignment format is called </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"http://genome.ucsc.edu/FAQ/FAQformat.html#format5"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">MAF (multiple alignment format)</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff right">. You can</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="html"><span class="idiff left">convert it to several other formats using </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"maf-convert.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">maf-convert</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff right">. You can make lastal produce a few other formats</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="html"><span class="idiff left">with option -f (see </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"lastal.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">lastal.html</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff right">)</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="html">0. If the strand is <span class="ni" style="color: #800080;">"</span>-<span class="ni" style="color: #800080;">"</span>, the start coordinate is <span class="idiff left right">the coordinate in</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="html"><span class="idiff left right">the reverse-complemented sequence (the same as if you were to</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="html"><span class="idiff left">reverse-complement the sequence before giving it to LAST).</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span><span class="idiff">You can convert MAF to other formats with </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"maf-convert.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">maf-convert</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff">, or use </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"lastal.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">lastal</span><span class="nt" style="color: #000080;"><span class="idiff right"></a></span></span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="html"><span class="idiff left">option </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-f</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right"> to get a few other formats</span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-2-compare-vertebrate-proteins-to-invertebrate-proteins"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 2: Compare vertebrate proteins to invertebrate proteins<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Use the lastdb -p option to indicate that the sequences are proteins:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"more-accurate-learn-substitution-gap-rates"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>More accurate: learn substitution <span class="ni" style="color: #800080;">&</span> gap rates<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>We can get more accurate alignments between the human and fugu</span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="html">mitochondrial genomes like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="html">lastdb -p -cR01 invdb invertebrate.fa</span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="html">lastal invdb vertebrate.fa</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="html">lastdb humdb humanMito.fa</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="html">last-train humdb fuguMito.fa <span class="ni" style="color: #800080;">></span> hufu.train</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="html">lastal -p hufu.train humdb fuguMito.fa <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></a></span> command finds the rates of deletion, insertion, and</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="html">each kind of substitution between these sequences, and writes them to</span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="html">a file <span class="ni" style="color: #800080;">"</span>hufu.train<span class="ni" style="color: #800080;">"</span>. lastal's <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-p<span class="nt" style="color: #000080;"></span></tt></span> option uses this file to get</span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="html">more-accurate alignments.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">example-3-compare-dna-sequences-to</span>-protein-sequences"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span><span class="idiff left right">Example 3: Compare DNA sequences to</span> protein sequences<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span><span class="idiff left right">Here we use the -F15 option, to specify translated alignment with a</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="html"><span class="idiff left right">score penalty of 15 for frameshift</span>s:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">comparing</span>-protein-sequences"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span><span class="idiff left right">Comparing</span> protein sequences<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span><span class="idiff left right">We can compare some query proteins to some reference proteins like</span></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="html"><span class="idiff left right">thi</span>s:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="html">lastdb -p -c<span class="idiff left right">R01 protdb protein</span>s.fa</span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="html">lastal <span class="idiff left right">-F15 protdb dnas.fa</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="html">lastdb -p -c<span class="idiff left right"> -R01 refdb ref-prot</span>s.fa</span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="html">lastal <span class="idiff left">refdb query-prots.fa </span><span class="ni" style="color: #800080;"><span class="idiff">></span></span><span class="idiff right"> prot-alns.maf</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-4-find-high-similarity-and-short-protein-alignments"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 4: Find high-similarity, and short, protein alignments<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST uses a <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-matrices.html"</span><span class="nt" style="color: #000080;">></span>scoring scheme<span class="nt" style="color: #000080;"></a></span> to find</span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="html">similarities. Some scoring schemes are tuned for weak similarities,</span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="html">others for strong similarities. The PAM30 scoring scheme finds strong</span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html">protein similarities:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-p<span class="nt" style="color: #000080;"></span></tt></span> tells it the sequences are proteins. (If you forget <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-p<span class="nt" style="color: #000080;"></span></tt></span> and</span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="html">the sequences look proteinaceous, you'll get a warning message.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The other options suppress alignments caused by simple sequence such</span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="html">as <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>APPSPAPPSPAPPSPAPPSPAP<span class="nt" style="color: #000080;"></tt></span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-R01<span class="nt" style="color: #000080;"></span></tt></span> converts the sequence letters to uppercase, then finds</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="html">simple regions and converts them to lowercase. This will be done</span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="html">for both ref-prots and query-prots.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-c<span class="nt" style="color: #000080;"></span></tt></span> omits alignments that lack a significant amount of</span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="html">uppercase-to-uppercase alignment.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You can also use <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></a></span>, but we've hardly tested it for</span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="html">protein-protein alignment, so we're not sure if it helps.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"find-high-similarity-and-short-protein-alignments"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Find high-similarity, and short, protein alignments<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If we just want high-similarity alignments, we can use the PAM30 (or</span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="html">PAM10) <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-matrices.html"</span><span class="nt" style="color: #000080;">></span>scoring scheme<span class="nt" style="color: #000080;"></a></span>:<span class="nt" style="color: #000080;"></p></span></span>
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388
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="html">lastdb -p -c<span class="idiff left right">R01 invdb invertebrate</span>.fa</span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="html">lastal -p<span class="idiff left right">PAM30 invdb vertebrate.fa</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="html">lastdb -p -c<span class="idiff left right"> -R01 refdb ref-prots</span>.fa</span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="html">lastal -p<span class="idiff left"> PAM30 refdb query-prots.fa </span><span class="ni" style="color: #800080;"><span class="idiff">></span></span><span class="idiff right"> prot-alns.maf</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This has two advantages:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>It omits weak alignments, or alignment parts (occasionally a strong</span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="html">similarity is flanked by a weak similarity).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>It omits low-similarity alignments, or alignment parts.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>It can find short similarities. If we seek very short similarities,</span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="html">weak ones are hopeless (statistically insignificant), so we had</span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="html">better focus on strong ones. (How short is <span class="ni" style="color: #800080;">"</span>very short<span class="ni" style="color: #800080;">"</span>? It</span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="html">depends on the amount of sequence data we are searching, but perhaps</span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="html">roughly less than 40 amino acids.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>It can find short similarities, which would be deemed insignificant</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="html">(likely to occur by chance between random sequences) unless we focus</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="html">the search on high-similarity.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-5-align-human-dna-sequences-to-the-human-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 5: Align human DNA sequences to the human genome<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>We can align human DNA sequences to the human genome like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"comparing-dna-to-proteins"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Comparing DNA to proteins<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>We can find related regions of DNA and proteins, allowing for nonsense</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="html">mutations and frameshifts. For example, let's find DNA regions</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="html">related to transposon proteins:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="html">lastdb -q -c -R01 trandb transposon-prots.fa</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="html">last-train --codon trandb dna.fa <span class="ni" style="color: #800080;">></span> codon.train</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="html">lastal -p codon.train -m100 -D1e9 -K1 trandb dna.fa <span class="ni" style="color: #800080;">></span> out.maf</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-q<span class="nt" style="color: #000080;"></span></tt></span> appends <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>*<span class="nt" style="color: #000080;"></tt></span> meaning STOP to each protein, and treats <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>*<span class="nt" style="color: #000080;"></tt></span> as</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="html">a 21st protein letter.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></tt></span> makes it do DNA-versus-protein. Here, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></a></span> tries</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="html">to learn 21x64 substitution rates, so it needs a fairly large amount</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="html">of data (e.g. a chromosome).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m100<span class="nt" style="color: #000080;"></span></tt></span> makes it more slow-and-sensitive than the default (which is</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m10<span class="nt" style="color: #000080;"></span></tt></span>), see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-D1e9<span class="nt" style="color: #000080;"></span></tt></span> sets a strict <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significance<span class="nt" style="color: #000080;"></a></span> threshold. It means: only</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="html">report strong similarities that would be expected to occur by chance,</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="html">between random sequences, at most once per 10^9 base-pairs. The</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="html">default is 1e6.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-K1<span class="nt" style="color: #000080;"></span></tt></span> streamlines the output by omitting any alignment whose DNA</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="html">range lies in that of a higher-scoring alignment.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Another possibility is to add <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-X1<span class="nt" style="color: #000080;"></span></tt></span>, which treats</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="html">matches to <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>X<span class="nt" style="color: #000080;"></tt></span> (unknown) amino acids as neutral instead of</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="html">disfavored.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-high-indel-error-long-dna-reads-to-a-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Aligning high-indel-error long DNA reads to a genome<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Suppose we have DNA reads in either FASTA or <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/nar/gkp1137"</span><span class="nt" style="color: #000080;">></span>FASTQ<span class="nt" style="color: #000080;"></a></span> format. This is</span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="html">sensitive but slow:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="html">lastdb -uNEAR -R01 humandb human/chr*.fa</span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="html">lastal humandb queries.fa | last-split <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="html">lastdb -P8 -uNEAR -R01 mydb genome.fa</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="html">last-train -P8 -Q0 mydb reads.fastq <span class="ni" style="color: #800080;">></span> reads.train</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="html">lastal -P8 -p reads.train mydb reads.fastq | last-split <span class="ni" style="color: #800080;">></span> out.maf</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This will use about 15 gigabytes of memory.<span class="nt" style="color: #000080;"></p></span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-P8<span class="nt" style="color: #000080;"></span></tt></span> uses 8 parallel threads, adjust as appropriate for your</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="html">computer. This has no effect on the results.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uNEAR<span class="nt" style="color: #000080;"></span></tt></span> selects a <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>seeding scheme<span class="nt" style="color: #000080;"></a></span> that's better at finding</span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="html">alignments with few substitutions and/or many gaps.<span class="nt" style="color: #000080;"></p></span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-Q0<span class="nt" style="color: #000080;"></span></tt></span> makes it discard the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/nar/gkp1137"</span><span class="nt" style="color: #000080;">></span>fastq<span class="nt" style="color: #000080;"></a></span> quality information (or you can</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="html">keep-but-ignore it with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-Qkeep<span class="nt" style="color: #000080;"></span></tt></span>).<span class="nt" style="color: #000080;"></p></span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-split.html"</span><span class="nt" style="color: #000080;">></span>last-split<span class="nt" style="color: #000080;"></a></span> finds a unique best alignment for each part of each read.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Here we used <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-R01<span class="nt" style="color: #000080;"></span></tt></span> to lowercase simple sequence like</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>cacacacacacacacacacacaca<span class="nt" style="color: #000080;"></tt></span>. But we didn't suppress it with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-c<span class="nt" style="color: #000080;"></span></tt></span>,</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="html">so as not to hide anything from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-split.html"</span><span class="nt" style="color: #000080;">></span>last-split<span class="nt" style="color: #000080;"></a></span>. If desired, you can</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="html">filter lowercase with <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-postmask.html"</span><span class="nt" style="color: #000080;">></span>last-postmask<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You can go faster by sacrificing a bit of sensitivity. It depends on</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html">your aim, e.g. slow-and-sensitive seems necessary to find intricate</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="html">rearrangements of repeats. Suggested ways to go faster:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-uNEAR selects a <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>seeding scheme<span class="nt" style="color: #000080;"></a></span> that makes it</span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="html">better at finding short-and-strong similarities. (It also changes</span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="html">the default scoring scheme.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md"</span><span class="nt" style="color: #000080;">></span>Mask repeats<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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417
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-R01 tells it to mark simple sequences (such as cacacacacacacacaca)</span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="html">by lowercase, but not suppress them. This has no effect on the</span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="html">alignment, but it allows us to see simple sequences in the output,</span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="html">and gives us the option to do <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-postmask.html"</span><span class="nt" style="color: #000080;">></span>post-alignment masking<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Add lastal option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-k8<span class="nt" style="color: #000080;"></span></tt></span> (or <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-k16<span class="nt" style="color: #000080;"></span></tt></span> etc). This makes it faster,</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="html">by only finding initial matches starting at every 8th (or 16th etc)</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="html">position in the reads.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span><span class="idiff left right">last-split reads the alignments produced by lastal, and looks for a</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="html"><span class="idiff left right">unique best alignment for each part of each query. It allows</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="html"><span class="idiff left right">different parts of one query to match different parts of the genome,</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="html"><span class="idiff left right">which may happen due to rearrangements. It has several useful</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="html"><span class="idiff left">options, please see </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"last-split.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">last-split.html</span><span class="nt" style="color: #000080;"><span class="idiff right"></a></span></span>.<span class="nt" style="color: #000080;"></p></span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span><span class="idiff left">Replace </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-uNEAR</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff"> with </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-uRY32</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff"> (or </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-uRY16</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff">, </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-uRY8</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right">,</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-uRY4</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right">). This makes it check for initial matches starting at</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="html"><span class="idiff left right">only ~1/32 (or ~1/16 etc) of positions, in both reads and genome.</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="html"><span class="idiff left">Compared to </span><span class="nt" style="color: #000080;"><span class="idiff"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-k</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right">: this harms sensitivity slightly more, but</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="html"><span class="idiff left right">reduces memory use and makes lastdb faster</span>.<span class="nt" style="color: #000080;"></p></span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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429
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"which-genome-version-to-use"</span><span class="nt" style="color: #000080;">></span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Which genome version to use?<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Some genome versions (e.g. for human) have artificial</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="html">exactly-duplicated regions, which makes it hard to align reads</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="html">uniquely. To avoid that, look for a genome version called something</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="html">like <span class="ni" style="color: #800080;">"</span>analysis set<span class="ni" style="color: #800080;">"</span>.<span class="nt" style="color: #000080;"></p></span></span>
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430
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"tuning-speed-sensitivity-memory-and-disk-usage"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Tuning speed, sensitivity, memory and disk usage<span class="nt" style="color: #000080;"></h2></span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>You can make LAST faster by <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-parallel.html"</span><span class="nt" style="color: #000080;">></span>using multiple CPUs<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>You can <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-tuning.html"</span><span class="nt" style="color: #000080;">></span>trade off speed, sensitivity, memory and disk usage<span class="nt" style="color: #000080;"></a></span>. To go much faster, try either lastal option</span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-k32<span class="nt" style="color: #000080;"></span></tt></span> or lastdb option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY32<span class="nt" style="color: #000080;"></span></tt></span> (but not both). <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-k32<span class="nt" style="color: #000080;"></span></tt></span> is a</span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="html">bit more sensitive, but <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY32<span class="nt" style="color: #000080;"></span></tt></span> uses less memory.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-low-error-long-dna-reads-to-a-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Aligning low-error long DNA reads to a genome<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>We can do this the same way as for high-error reads, but perhaps</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="html">accelerate more aggressively (e.g. <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY32<span class="nt" style="color: #000080;"></span></tt></span>).<span class="nt" style="color: #000080;"></p></span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If repeats are not masked, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-C2<span class="nt" style="color: #000080;"></span></tt></span> may reduce run time</span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="html">with little effect on accuracy.<span class="nt" style="color: #000080;"></p></span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-potentially-spliced-rna-or-cdna-long-reads-to-a-genome"</span><span class="nt" style="color: #000080;">></span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Aligning potentially-spliced RNA or cDNA long reads to a genome<span class="nt" style="color: #000080;"></h3></span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>. (For low-error reads, you can probably omit <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-d90<span class="nt" style="color: #000080;"></span></tt></span> and</span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m20<span class="nt" style="color: #000080;"></span></tt></span>.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-6-find-very-short-dna-alignments"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 6: Find very short DNA alignments<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>By default, LAST is quite strict, and only reports significant</span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="html">alignments that will rarely occur by chance. In the preceding</span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="html">example, the minimum alignment length is about 26 bases (less for</span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="html">smaller genomes). To find shorter alignments, we must down-tune the</span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="html">strictness:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-illumina-dna-reads-to-a-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Aligning Illumina DNA reads to a genome<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="html">lastdb -uNEAR -R01 humandb human/chr*.fa</span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="html">lastal -D100 humandb queries.fa | last-split <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="html">lastdb -P8 -uNEAR -R01 -C2 mydb genome.fasta</span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html">last-train -P8 -Q1 mydb reads.fastq.gz <span class="ni" style="color: #800080;">></span> reads.train</span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="html">lastal -P8 -p reads.train mydb reads.fastq.gz | last-split <span class="ni" style="color: #800080;">></span> out.maf</span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>-D100 makes lastal report alignments that could occur by chance once</span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="html">per hundred query letters. (The default is once per million.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>In this example, the minimum alignment length is about 20 bases (less</span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="html">for smaller genomes).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Most LAST commands accept gzip-compressed (<span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>.gz<span class="nt" style="color: #000080;"></tt></span>) files.<span class="nt" style="color: #000080;"></p></span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastdb.html"</span><span class="nt" style="color: #000080;">></span>lastdb<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-C2<span class="nt" style="color: #000080;"></span></tt></span> makes the alignment a bit faster, but uses more</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="html">memory. This has no effect on the results. (You could use it in the</span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="html">other examples too, but it might not be faster.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-Q1<span class="nt" style="color: #000080;"></span></tt></span> makes it use the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/nar/gkp1137"</span><span class="nt" style="color: #000080;">></span>fastq<span class="nt" style="color: #000080;"></a></span> quality information to improve the</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="html">training and alignment. LAST <span class="nt" style="color: #000080;"><strong></span>assumes<span class="nt" style="color: #000080;"></strong></span> that the qualities reflect</span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="html">substitution errors, not insertion/deletion errors. (For long</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="html">non-Illumina reads, we suspect this assumption doesn't hold, so we</span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="html">didn't use this option.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This recipe may be excessively slow-and-sensitive. Adding <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html">option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-C2<span class="nt" style="color: #000080;"></span></tt></span> may make it faster with negligible accuracy loss. You</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="html">can accelerate with e.g. <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY16<span class="nt" style="color: #000080;"></span></tt></span> or <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-k16<span class="nt" style="color: #000080;"></span></tt></span> as above.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"finding-very-short-dna-alignments"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Finding very short DNA alignments<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>By default, LAST only reports <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significant<span class="nt" style="color: #000080;"></a></span> alignments that will rarely</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="html">occur by chance. In the preceding example, the minimum alignment</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="html">length is about 26 bases for a human-size genome (less for smaller</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="html">genomes). To find shorter alignments, add <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-D100<span class="nt" style="color: #000080;"></span></tt></span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="html">(say), to get alignments that could occur by chance once per hundred</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="html">query letters (the default is once per million.) This makes the</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="html">minimum alignment length about 20 bases for a human-size genome.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">example-7-align-human-fastq-sequences-to-the-human</span>-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="html"><span class="nt" style="color: #000080;"><h<span class="idiff left">2></span></span><span class="idiff">Example 7: Align human fastq sequences to the human genome</span><span class="nt" style="color: #000080;"><span class="idiff right"></h2</span>></span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span><span class="idiff left right">DNA sequences are not always perfectly accurate, and they are</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="html"><span class="idiff left right">sometimes provided in fastq format, which indicates the reliability of</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="html"><span class="idiff left right">each base. LAST can use this information to improve alignment</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="html"><span class="idiff left right">accuracy. Option -Q1 indicates fastq-sanger format</span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">aligning-paired-end-illumina-dna-reads-to-a</span>-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="html"><span class="nt" style="color: #000080;"><h<span class="idiff left">3></span></span><span class="idiff">Aligning paired-end Illumina DNA reads to a genome</span><span class="nt" style="color: #000080;"><span class="idiff right"></h3</span>></span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span><span class="idiff left">You could use </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"last-pair-probs.html"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">last-pair-probs</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff right">. It has a disadvantage: it doesn't</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="html"><span class="idiff left">allow different parts of one read (i.e. one </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">end</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right">) to align to</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="html"><span class="idiff left right">different parts of the genome. Alternatively, you could align the</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="html"><span class="idiff left right">reads individually, ignoring the pair relationships</span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="html">lastdb -uNEAR -R01 humandb human/chr*.fa</span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="html">lastal -Q1 humandb queries.fastq | last-split <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="html">fastq-interleave reads1.fq reads2.fq | lastal -P8 -p reads.train mydb | last-split <span class="ni" style="color: #800080;">></span> out.maf</span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Assumption:<span class="nt" style="color: #000080;"></strong></span> LAST assumes the reliabilities reflect substitution</span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="html">errors, not insertion/deletion errors. If that is not true, you can</span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="html">tell it to ignore the reliability data with -Q0.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>fastq-interleave<span class="nt" style="color: #000080;"></span></tt></span> ensures that each read has a unique name (by</span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="html">appending <span class="ni" style="color: #800080;">"</span>/1<span class="ni" style="color: #800080;">"</span> and <span class="ni" style="color: #800080;">"</span>/2<span class="ni" style="color: #800080;">"</span> if necessary).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"fastq-format-confusion"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Fastq format confusion<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Unfortunately, there is more than one fastq format (see</span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://nar.oxfordjournals.org/content/38/6/1767.long"</span><span class="nt" style="color: #000080;">></span>http://nar.oxfordjournals.org/content/38/6/1767.long<span class="nt" style="color: #000080;"></a></span>). Recently</span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="html">(2013) fastq-sanger seems to be dominant, but if you have another</span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="html">variant you need to change the -Q option (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-potentially-spliced-illumina-reads-to-a-genome"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Aligning potentially-spliced Illumina reads to a genome<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-split.html"</span><span class="nt" style="color: #000080;">></span>last-split<span class="nt" style="color: #000080;"></a></span> (and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-pair-probs.html"</span><span class="nt" style="color: #000080;">></span>last-pair-probs<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"paired-dna-reads"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Paired DNA reads<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you have paired DNA reads, there are two options:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="html"><span class="nt" style="color: #000080;"><ol</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"arabic"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Use last-pair-probs (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-pair-probs.html"</span><span class="nt" style="color: #000080;">></span>last-pair-probs.html<span class="nt" style="color: #000080;"></a></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Ignore the pairing information, and align the reads individually</span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="html">(using last-split as above). This may be useful because</span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="html">last-pair-probs does not currently allow different parts of one</span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="html">read to match different parts of the genome, though it does allow</span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="html">the two reads in a pair to match (e.g.) different chromosomes.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-8-compare-the-human-and-mouse-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 8: Compare the human and mouse genomes<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/mcfrith/last-genome-alignments"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-human-chimp-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Aligning human <span class="ni" style="color: #800080;">&</span> chimp genomes<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>This is very slow-and-sensitive:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="html">lastdb -P8 -uNEAR -R01 humdb human_no_alt_analysis_set.fa</span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="html">last-train -P8 --revsym -E0.05 -C2 humdb chimp.fa <span class="ni" style="color: #800080;">></span> humchi.train</span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="html">lastal -E0.05 -C2 -p humchi.train humdb chimp.fa | last-split <span class="ni" style="color: #800080;">></span> humchi1.maf</span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--revsym<span class="nt" style="color: #000080;"></span></tt></span> makes the substitution rates the same on both strands.</span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="html">For example, it makes A→G equal T→C (because A→G on one strand means</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="html">T→C on the other strand). This is usually appropriate for</span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="html">genome-genome comparison (but maybe not for mitochondria which have</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="html">asymmetric <span class="ni" style="color: #800080;">"</span>heavy<span class="ni" style="color: #800080;">"</span> and <span class="ni" style="color: #800080;">"</span>light<span class="ni" style="color: #800080;">"</span> strands).<span class="nt" style="color: #000080;"></p></span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="html"><span class="nt" style="color: #000080;"><p><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-E0.05<span class="nt" style="color: #000080;"></span></tt></span> means only get <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significant<span class="nt" style="color: #000080;"></a></span> alignments that would be</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="html">expected to occur by chance at a rate ≤ 0.05 times per pair of random</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="html">sequences of length 1 billion each.<span class="nt" style="color: #000080;"></p></span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The result so far is asymmetric: each part of the chimp genome is</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="html">aligned to at most one part of the human genome, but not vice-versa.</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="html">We can get one-to-one alignments like this:<span class="nt" style="color: #000080;"></p></span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="html">maf-swap humchi1.maf | last-split <span class="ni" style="color: #800080;">></span> humchi2.maf</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Then we can discard less-confident alignments, and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"maf-convert.html"</span><span class="nt" style="color: #000080;">></span>convert<span class="nt" style="color: #000080;"></a></span> to a</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="html">compact tabular format:<span class="nt" style="color: #000080;"></p></span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="html">last-postmask humchi2.maf | maf-convert -n tab | awk -F= '$2 <span class="ni" style="color: #800080;"><</span>= 1e-5' <span class="ni" style="color: #800080;">></span> humchi.tab</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-postmask.html"</span><span class="nt" style="color: #000080;">></span>last-postmask<span class="nt" style="color: #000080;"></a></span> discards alignments caused by simple sequence. The</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">></span>awk<span class="nt" style="color: #000080;"></tt></span> command gets alignments with <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-split.html"</span><span class="nt" style="color: #000080;">></span>mismap probability<span class="nt" style="color: #000080;"></a></span> ≤ 10^-5.</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="html">Finally, we can make a <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-dotplot.html"</span><span class="nt" style="color: #000080;">></span>dotplot<span class="nt" style="color: #000080;"></a></span>:<span class="nt" style="color: #000080;"></p></span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="html">last-dotplot humchi.tab humchi.png</span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To go faster, with minor accuracy loss: replace <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uNEAR<span class="nt" style="color: #000080;"></span></tt></span> with</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="html"><span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY32<span class="nt" style="color: #000080;"></span></tt></span> and/or <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md"</span><span class="nt" style="color: #000080;">></span>mask repeats<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To squeeze out the last 0.000...1% of accuracy: add <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m50<span class="nt" style="color: #000080;"></span></tt></span> to the</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span> options.<span class="nt" style="color: #000080;"></p></span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"aligning-human-mouse-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="html"><span class="nt" style="color: #000080;"><h3></span>Aligning human <span class="ni" style="color: #800080;">&</span> mouse genomes<span class="nt" style="color: #000080;"></h3></span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You can do this in the same way as human/chimp, except that <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uNEAR<span class="nt" style="color: #000080;"></span></tt></span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="html">should be omitted. To increase sensitivity, but also time and memory</span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="html">use, add lastdb <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>seeding<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uMAM4<span class="nt" style="color: #000080;"></span></tt></span> or or <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uMAM8<span class="nt" style="color: #000080;"></span></tt></span>. To</span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="html">increase them even more, add <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-m100<span class="nt" style="color: #000080;"></span></tt></span> (or as high as</span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="html">you can bear).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"example-9-compare-the-human-and-chimp-genomes"</span><span class="nt" style="color: #000080;">></span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Example 9: Compare the human and chimp genomes<span class="nt" style="color: #000080;"></h2></span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/mcfrith/last-genome-alignments"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>. But</span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="html">that recipe is <span class="nt" style="color: #000080;"><em></span>extremely<span class="nt" style="color: #000080;"></em></span> slow-and-accurate. You can <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-tuning.html"</span><span class="nt" style="color: #000080;">></span>tune<span class="nt" style="color: #000080;"></a></span> it to compare huge, high-similarity genomes with</span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="html">moderate run time and memory use:<span class="nt" style="color: #000080;"></p></span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"large-reference-sequences"</span><span class="nt" style="color: #000080;">></span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Large reference sequences<span class="nt" style="color: #000080;"></h2></span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If the sequences that you give to lastdb exceed ~4 billion letters,</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="html">consider using 8-byte LAST (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastdb.html"</span><span class="nt" style="color: #000080;">></span>lastdb8<span class="nt" style="color: #000080;"></a></span> and <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal8<span class="nt" style="color: #000080;"></a></span>). Ordinary (4-byte)</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="html">LAST can't handle so much sequence at once, so <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastdb.html"</span><span class="nt" style="color: #000080;">></span>lastdb<span class="nt" style="color: #000080;"></a></span> splits it into</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="html"><span class="ni" style="color: #800080;">"</span>volumes<span class="ni" style="color: #800080;">"</span>, which may be inefficient. 8-byte LAST avoids voluming, but</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="html">uses more memory. So <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastdb.html"</span><span class="nt" style="color: #000080;">></span>lastdb8<span class="nt" style="color: #000080;"></a></span> works well with a memory-reducing</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="html">option: <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY<span class="nt" style="color: #000080;"></span></tt></span> or <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-w<span class="nt" style="color: #000080;"></span></tt></span> or <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-W<span class="nt" style="color: #000080;"></span></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"moar-faster"</span><span class="nt" style="color: #000080;">></span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Moar faster<span class="nt" style="color: #000080;"></h2></span></span>
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505
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Omit the sensitivity-boosting lastal -m option.<span class="nt" style="color: #000080;"></p></span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Replace <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uNEAR<span class="nt" style="color: #000080;"></span></tt></span> with <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-uRY32<span class="nt" style="color: #000080;"></span></tt></span>.<span class="nt" style="color: #000080;"></p></span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-parallel.html"</span><span class="nt" style="color: #000080;">></span>Using multiple CPUs / cores<span class="nt" style="color: #000080;"></a></p></span></span>
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509
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>If the <span class="ni" style="color: #800080;">"</span>reference<span class="ni" style="color: #800080;">"</span> genome (the one given to lastdb) is <span class="ni" style="color: #800080;">></span> 4 GB, it's</span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="html">probably more efficient to use lastdb8 and lastal8, instead of</span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="html">lastdb and lastal.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-tuning.html"</span><span class="nt" style="color: #000080;">></span>Various speed <span class="ni" style="color: #800080;">&</span> memory options<span class="nt" style="color: #000080;"></a></p></span></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">example-10-</span>ambiguity-of-alignment-columns"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span><span class="idiff left right">Example 10: </span>Ambiguity of alignment columns<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"ambiguity-of-alignment-columns"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Ambiguity of alignment columns<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Consider this alignment:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="html">TGAAGTTAAAGGTATATGAATTCCAATTCTTAACCCCCCTATTAAACGAATATCTTG</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">@@ -522,12 +622,10 @@ TGAAGTTAAAGGTATATGAATTCCAATTCTTAACCCCCCTATTAAACGAATATCTTG</td>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="html">TGAAGTTAGAGGTAT--GGTTTTGAGTAGT----CCTCCTATTTTTCGAATATCTTG</span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The middle section has such weak similarity that its precise alignment</span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="html">cannot be confidently inferred.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>It is sometimes useful to estimate the ambiguity of each column in an</span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="html">alignment. We can do that using lastal option -j4:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="html">cannot be confidently inferred. We can see the confidence of each</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="html">alignment column with <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal<span class="nt" style="color: #000080;"></a></span> option <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-j4<span class="nt" style="color: #000080;"></span></tt></span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="html">lastdb -cR01 humdb humanMito.fa</span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="html">lastal -j4 humdb fuguMito.fa <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="html">lastal -j4 -p hufu.train humdb fuguMito.fa <span class="ni" style="color: #800080;">></span> myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The output looks like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></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">@@ -537,7 +635,7 @@ s seqY 0 51 + 51 TGAAGTTAGAGGTAT--GGTTTTGAGTAGT----CCTCCTATTTTTCGAATATCTTG</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="html">p %*.14442011.(%##<span class="ni" style="color: #800080;">"</span>%$$$$###<span class="ni" style="color: #800080;">""</span>!!!<span class="ni" style="color: #800080;">""""&</span>'(*,340.,,.~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The <span class="ni" style="color: #800080;">"</span>p<span class="ni" style="color: #800080;">"</span> line indicates the probability that each column is wrongly</span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="html">aligned, using a compact code (the same as <span class="idiff left right">fastq-sanger</span> format):<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="html">aligned, using a compact code (the same as <span class="nt" style="color: #000080;"><span class="idiff left"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"reference external"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://doi.org/10.1093/nar/gkp1137"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">fastq</span><span class="nt" style="color: #000080;"><span class="idiff right"></a></span></span> format):<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="html"><span class="nt" style="color: #000080;"><table</span> <span class="na" style="color: #008080;">border=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="html"><span class="nt" style="color: #000080;"><colgroup></span></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">@@ -633,8 +731,6 @@ aligned, using a compact code (the same as fastq-sanger format):</p></td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Note that each alignment is grown from a <span class="ni" style="color: #800080;">"</span>core<span class="ni" style="color: #800080;">"</span> region, and the</span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="html">ambiguity estimates assume that the core is correctly aligned. The</span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="html">core is indicated by <span class="ni" style="color: #800080;">"</span>~<span class="ni" style="color: #800080;">"</span> symbols, and it contains exact matches only.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST has options to find alignments with optimal column probabilities,</span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="html">instead of optimal score: see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"lastal.html"</span><span class="nt" style="color: #000080;">></span>lastal.html<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#f9d530bbfca92a35437d8018b31c3726538723db"><strong>doc/last-tutorial.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">LAST <span class="idiff left right">Tutorial</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">LAST <span class="idiff left right">Cookbook</span></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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">LAST finds similar regions between sequences, and aligns them.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">LAST_ is used by running commands in a terminal / command line. It</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">has many options: unfortunately, the LAST developers don't know the</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">best options for every possible alignment task. Here are some</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">reasonable starting points. Feel free to optimize (and share!) search</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">protocols.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">Example 1: Compare the human and</span> fugu mitochondrial genomes</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">-----------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">A minimal example: compare human &</span> fugu mitochondrial genomes</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">-----------------------------------------------------------<span class="idiff left right">--</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">For our first example, we wish to find and align similar regions</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">between the human and fugu mitochondrial genomes. You can find these</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">sequences in the examples directory: humanMito.fa and fuguMito.fa. We</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"><span class="idiff left right">can compare them like th</span>is::</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">Let's find and align similar regions between the human and fugu</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"><span class="idiff left right">mitochondrial genomes. These FASTA-format files are in LAST's</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"><span class="idiff left right">examples directory: humanMito.fa and fuguMito.fa. The simplest</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">possible usage </span>is::</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> lastdb <span class="idiff left right">-cR01 </span>humdb humanMito.fa</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> lastdb humdb humanMito.fa</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> lastal humdb fuguMito.fa > myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">The lastdb command creates several files whose names begin with</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">"humdb". The lastal command then compares fuguMito.fa to the humdb</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">The lastdb<span class="idiff left right">_</span> command creates several files whose names begin with</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">"humdb". The lastal<span class="idiff left right">_</span> command then compares fuguMito.fa to the humdb</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">files, and writes the alignments to a file called "myalns.maf".</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">The "-cR01" option suppresses alignments caused by simple sequence</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">such as cacacacacacacacacacacaca.</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Understanding the output</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">------------------------</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">The output has very long lines, so you need to view it without</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">line-wrapping. For example, with a Unix/Linux/MacOsX command line,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">you can use::</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">line-wrapping. For example, you can use::</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> less -S myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">Each alignment looks like this::</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Each alignment looks like this<span class="idiff left right"> (MAF_ format)</span>::</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> a score=27 EG2=4.7e+04 E=2.6e-05</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> s humanMito 2170 145 + 16571 AGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTT...</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> s fuguMito 1648 142 + 16447 AGTAGGCTTAGAAGCAGCCACCA--CAAGAAAGCGTT...</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">The score is a measure of how significant the similarity is. EG2 and</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">E are explained at <span class="idiff left right">`<last-evalues.html>`_. Lines starting with "s"</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"><span class="idiff left right">contain: the sequence name, the start coordinate of the alignment, the</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"><span class="idiff left right">number of bases spanned by the alignment, the strand, the sequence</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"><span class="idiff left right">length, </span>and the aligned bases.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">E are explained at <span class="idiff left right">last-evalues_. Lines starting with "s" contain:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"><span class="idiff left right">the sequence name, the start coordinate of the alignment, the number</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"><span class="idiff left right">of bases spanned by the alignment, the strand, the sequence length,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">and the aligned bases.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">The start coordinates are zero-based. This means that, if the</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">alignment begins right at the start of a sequence, the coordinate is</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">0. If the strand is "-", the start coordinate is in the reverse</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">strand.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">0. If the strand is "-", the start coordinate is the coordinate in</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">the reverse-complemented sequence (the same as if you were to</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">reverse-complement the sequence before giving it to LAST).</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">You can convert MAF to other formats with maf-convert_, or use lastal_</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">option ``-f`` to get a few other formats.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">More accurate: learn substitution & gap rates</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">---------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">We can get more accurate alignments between the human and fugu</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">mitochondrial genomes like this::</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> lastdb humdb humanMito.fa</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> last-train humdb fuguMito.fa > hufu.train</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> lastal -p hufu.train humdb fuguMito.fa > myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">This alignment format is called `MAF (multiple alignment format)</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"><http://genome.ucsc.edu/FAQ/FAQformat.html#format5>`_. You can</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">convert it to several other formats using `maf-convert</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"><maf-convert.html>`_. You can make lastal produce a few other formats</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">with option -f (see `<lastal.html>`_).</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">The last-train_ command finds the rates of deletion, insertion, and</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">each kind of substitution between these sequences, and writes them to</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">a file "hufu.train". lastal's ``-p`` option uses this file to get</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">more-accurate alignments.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"><span class="idiff left right">Example 2: Compare vertebrate proteins to invertebrate protein</span>s</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">---------------------------<span class="idiff left right">------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"><span class="idiff left right">Comparing protein sequence</span>s</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">---------------------------</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Use the lastdb -p option to indicate that the sequences are proteins::</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">We can compare some query proteins to some reference proteins like</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">this::</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> lastdb -p -c<span class="idiff left right">R01 invdb invertebrate</span>.fa</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> lastal <span class="idiff left right">invdb vertebrate.fa</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> lastdb -p -c<span class="idiff left right"> -R01 refdb ref-prots</span>.fa</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> lastal <span class="idiff left right">refdb query-prots.fa > prot-alns.maf</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"><span class="idiff left right">Example 3: Compare DNA sequences to protein sequences</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"><span class="idiff left right">-----------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"><span class="idiff left right">``-p`` tells it the sequences are proteins. (If you forget ``-p`` and</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"><span class="idiff left right">the sequences look proteinaceous, you'll get a warning message.)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"><span class="idiff left right">Here we use the -F15 option, to specify translated alignment with a</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"><span class="idiff left right">score penalty of 15 for frameshifts:</span>:</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"><span class="idiff left right">The other options suppress alignments caused by simple sequence such</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"><span class="idiff left right">as ``APPSPAPPSPAPPSPAPPSPAP``</span>:</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> lastdb -p -cR01 protdb proteins.fa</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> lastal -F15 protdb dnas.fa</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">* ``-R01`` converts the sequence letters to uppercase, then finds</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> simple regions and converts them to lowercase. This will be done</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> for both ref-prots and query-prots.</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"><span class="idiff left right">Example 4: Find high-similarity, and short, protein alignments</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"><span class="idiff left right">--------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"><span class="idiff left right">* ``-c`` omits alignments that lack a significant amount of</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"><span class="idiff left right"> uppercase-to-uppercase alignment.</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">LAST uses a `scoring scheme <last-matrices.html>`_ to find</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">similarities. Some scoring schemes are tuned for weak similarities,</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">others for strong similarities. The PAM30 scoring scheme finds strong</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">protein similarities::</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">You can also use last-train_, but we've hardly tested it for</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">protein-protein alignment, so we're not sure if it helps.</span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> lastdb -p -cR01 invdb invertebrate.fa</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> lastal -pPAM30 invdb vertebrate.fa</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Find high-similarity, and short, protein alignments</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">If we just want high-similarity alignments, we can use the PAM30 (or</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">PAM10) `scoring scheme`_::</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> lastdb -p -c -R01 refdb ref-prots.fa</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> lastal -p PAM30 refdb query-prots.fa > prot-alns.maf</span>
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83
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">This has two advantages:</span>
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85
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">* It omits weak alignments, or alignment parts (occasionally a strong</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> similarity is flanked by a weak similarity).</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">* It omits low-similarity alignments, or alignment parts.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">* It can find short similarities, which would be deemed insignificant</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> (likely to occur by chance between random sequences) unless we focus</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> the search on high-similarity.</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">Comparing DNA to proteins</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">-------------------------</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">We can find related regions of DNA and proteins, allowing for nonsense</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">mutations and frameshifts. For example, let's find DNA regions</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">related to transposon proteins::</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> lastdb -q -c -R01 trandb transposon-prots.fa</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> last-train --codon trandb dna.fa > codon.train</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> lastal -p codon.train -m100 -D1e9 -K1 trandb dna.fa > out.maf</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">``-q`` appends ``*`` meaning STOP to each protein, and treats ``*`` as</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">a 21st protein letter.</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">``--codon`` makes it do DNA-versus-protein. Here, last-train_ tries</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">to learn 21x64 substitution rates, so it needs a fairly large amount</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">of data (e.g. a chromosome).</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">``-m100`` makes it more slow-and-sensitive than the default (which is</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">``-m10``), see lastal_.</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">``-D1e9`` sets a strict significance_ threshold. It means: only</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">report strong similarities that would be expected to occur by chance,</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">between random sequences, at most once per 10^9 base-pairs. The</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">default is 1e6.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">``-K1`` streamlines the output by omitting any alignment whose DNA</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">range lies in that of a higher-scoring alignment.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">Another possibility is to add last-train_ option ``-X1``, which treats</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">matches to ``X`` (unknown) amino acids as neutral instead of</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">disfavored.</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Aligning high-indel-error long DNA reads to a genome</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">----------------------------------------------------</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">Suppose we have DNA reads in either FASTA or FASTQ_ format. This is</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">sensitive but slow::</span>
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88
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">* It can find short similarities. If we seek very short similarities,</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> weak ones are hopeless (statistically insignificant), so we had</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> better focus on strong ones. (How short is "very short"? It</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> depends on the amount of sequence data we are searching, but perhaps</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> roughly less than 40 amino acids.)</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> lastdb -P8 -uNEAR -R01 mydb genome.fa</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> last-train -P8 -Q0 mydb reads.fastq > reads.train</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> lastal -P8 -p reads.train mydb reads.fastq | last-split > out.maf</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"><span class="idiff left right">Example 5: Align human DNA sequences to the human genome</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"><span class="idiff left right">--------------------------------------------------------</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"><span class="idiff left right">``-P8`` uses 8 parallel threads, adjust as appropriate for your</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><span class="idiff left right">computer. This has no effect on the results.</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">We can align human DNA sequences to the human genome like this::</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">``-uNEAR`` selects a `seeding scheme`_ that's better at finding</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">alignments with few substitutions and/or many gaps.</span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"><span class="idiff left right"> lastdb -uNEAR -R01 humandb human/chr*.fa</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"><span class="idiff left right"> lastal humandb queries.fa | last-split > myalns.maf</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"><span class="idiff left right">``-Q0`` makes it discard the fastq_ quality information (or you can</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"><span class="idiff left right">keep-but-ignore it with ``-Qkeep``).</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"><span class="idiff left right">This will use about 15 gigabytes of memory</span>.</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"><span class="idiff left right">last-split_ finds a unique best alignment for each part of each read</span>.</span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">* -uNEAR selects a `seeding scheme <last-seeds.html>`_ that makes it</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> better at finding short-and-strong similarities. (It also changes</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> the default scoring scheme.)</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">Here we used ``-R01`` to lowercase simple sequence like</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">``cacacacacacacacacacacaca``. But we didn't suppress it with ``-c``,</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">so as not to hide anything from last-split_. If desired, you can</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">filter lowercase with last-postmask_.</span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">* -R01 tells it to mark simple sequences (such as cacacacacacacacaca)</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> by lowercase, but not suppress them. This has no effect on the</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> alignment, but it allows us to see simple sequences in the output,</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> and gives us the option to do `post-alignment masking</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> <last-postmask.html>`_.</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">You can go faster by sacrificing a bit of sensitivity. It depends on</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">your aim, e.g. slow-and-sensitive seems necessary to find intricate</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">rearrangements of repeats. Suggested ways to go faster:</span>
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114
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">* last-split reads the alignments produced by lastal, and looks for a</span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> unique best alignment for each part of each query. It allows</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"> different parts of one query to match different parts of the genome,</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> which may happen due to rearrangements. It has several useful</span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> options, please see `<last-split.html>`_.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">* `Mask repeats`_.</span>
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120
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">Tuning speed, sensitivity, memory and disk usage</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">------------------------------------------------</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">* Add lastal option ``-k8`` (or ``-k16`` etc). This makes it faster,</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> by only finding initial matches starting at every 8th (or 16th etc)</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> position in the reads.</span>
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123
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">* You can make LAST faster by `using multiple CPUs</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext"> <last-parallel.html>`_.</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">* Replace ``-uNEAR`` with ``-uRY32`` (or ``-uRY16``, ``-uRY8``,</span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> ``-uRY4``). This makes it check for initial matches starting at</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> only ~1/32 (or ~1/16 etc) of positions, in both reads and genome.</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> Compared to ``-k``: this harms sensitivity slightly more, but</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> reduces memory use and makes lastdb faster.</span>
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126
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">* You can `trade off speed, sensitivity, memory and disk usage</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> <last-tuning.html>`_. To go much faster, try either lastal option</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"> ``-k32`` or lastdb option ``-uRY32`` (but not both). ``-k32`` is a</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> bit more sensitive, but ``-uRY32`` uses less memory.</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">Which genome version to use?</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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131
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">Example 6: Find very short DNA alignments</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">-----------------------------------------</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">Some genome versions (e.g. for human) have artificial</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">exactly-duplicated regions, which makes it hard to align reads</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">uniquely. To avoid that, look for a genome version called something</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">like "analysis set".</span>
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134
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext"></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">By default, LAST is quite strict, and only reports significant</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">alignments that will rarely occur by chance. In the preceding</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">example, the minimum alignment length is about 26 bases (less for</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">smaller genomes). To find shorter alignments, we must down-tune the</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">strictness::</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">Aligning low-error long DNA reads to a genome</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"><span class="idiff left right"> lastdb -uNEAR -R01 humandb human/chr*.fa</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"><span class="idiff left right"> lastal -D100 humandb queries.fa | last-split > myalns.maf</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"><span class="idiff left right">We can do this the same way as for high-error reads, but perhaps</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"><span class="idiff left right">accelerate more aggressively (e.g. ``-uRY32``).</span></span>
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143
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"><span class="idiff left right">* -D100 makes lastal report alignments that could occur by chance onc</span>e</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"><span class="idiff left right"> per hundred query letters. (The default is once per million.)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"><span class="idiff left right">If repeats are not masked, lastal_ option ``-C2`` may reduce run tim</span>e</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"><span class="idiff left right">with little effect on accuracy.</span></span>
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146
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"><span class="idiff left right">In this example, the minimum alignment length is about 20 bases (less</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"><span class="idiff left right">for smaller genomes).</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"><span class="idiff left right">Aligning potentially-spliced RNA or cDNA long reads to a genome</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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149
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"><span class="idiff left right">Example 7: Align human fastq sequences to the human genome</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"><span class="idiff left right">----------------------------------------------------------</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"><span class="idiff left right">See here_. (For low-error reads, you can probably omit ``-d90`` and</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"><span class="idiff left right">``-m20``.)</span></span>
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152
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">DNA sequences are not always perfectly accurate, and they are</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">sometimes provided in fastq format, which indicates the reliability of</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">each base. LAST can use this information to improve alignment</span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">accuracy. Option -Q1 indicates fastq-sanger format::</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">Aligning Illumina DNA reads to a genome</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">---------------------------------------</span>
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157
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> lastdb -uNEAR -R01 humandb human/chr*.fa</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> lastal -Q1 humandb queries.fastq | last-split > myalns.maf</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">::</span>
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160
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"><span class="idiff left right">**Assumption:** LAST assumes the reliabilities reflect substitution</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"><span class="idiff left right">errors, not insertion/deletion errors. If that is not true, you ca</span>n</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"><span class="idiff left right">tell it to ignore the reliability data with -Q0.</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"><span class="idiff left right"> lastdb -P8 -uNEAR -R01 -C2 mydb genome.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"><span class="idiff left right"> last-train -P8 -Q1 mydb reads.fastq.gz > reads.trai</span>n</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"><span class="idiff left right"> lastal -P8 -p reads.train mydb reads.fastq.gz | last-split > out.maf</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">Fastq format confusion</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">----------------------</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">Most LAST commands accept gzip-compressed (``.gz``) files.</span>
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167
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">Unfortunately, there is more than one fastq format (see</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext">http://nar.oxfordjournals.org/content/38/6/1767.long). Recently</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">(2013) fastq-sanger seems to be dominant, but if you have another</span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">variant you need to change the -Q option (see `<lastal.html>`_).</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">lastdb_ option ``-C2`` makes the alignment a bit faster, but uses more</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">memory. This has no effect on the results. (You could use it in the</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">other examples too, but it might not be faster.)</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext">Paired DNA reads</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">----------------</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">``-Q1`` makes it use the fastq_ quality information to improve the</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">training and alignment. LAST **assumes** that the qualities reflect</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">substitution errors, not insertion/deletion errors. (For long</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">non-Illumina reads, we suspect this assumption doesn't hold, so we</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">didn't use this option.)</span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">If you have paired DNA reads, there are two options:</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">This recipe may be excessively slow-and-sensitive. Adding lastal_</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">option ``-C2`` may make it faster with negligible accuracy loss. You</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">can accelerate with e.g. ``-uRY16`` or ``-k16`` as above.</span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext">1. Use last-pair-probs (see `<last-pair-probs.html>`_).</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">Finding very short DNA alignments</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext">2. Ignore the pairing information, and align the reads individually</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> (using last-split as above). This may be useful because</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> last-pair-probs does not currently allow different parts of one</span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> read to match different parts of the genome, though it does allow</span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> the two reads in a pair to match (e.g.) different chromosomes.</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">By default, LAST only reports significant_ alignments that will rarely</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">occur by chance. In the preceding example, the minimum alignment</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">length is about 26 bases for a human-size genome (less for smaller</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">genomes). To find shorter alignments, add lastal_ option ``-D100``</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">(say), to get alignments that could occur by chance once per hundred</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">query letters (the default is once per million.) This makes the</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">minimum alignment length about 20 bases for a human-size genome.</span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"><span class="idiff left right">Example 8: Compare the human and mouse genomes</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"><span class="idiff left right">----------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"><span class="idiff left right">Aligning paired-end Illumina DNA reads to a genome</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext">See `here <https://github.com/mcfrith/last-genome-alignments>`_.</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">You could use last-pair-probs_. It has a disadvantage: it doesn't</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">allow different parts of one read (i.e. one "end") to align to</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">different parts of the genome. Alternatively, you could align the</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">reads individually, ignoring the pair relationships::</span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext">Example 9: Compare the human and chimp genomes</span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext">----------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> fastq-interleave reads1.fq reads2.fq | lastal -P8 -p reads.train mydb | last-split > out.maf</span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">See `here <https://github.com/mcfrith/last-genome-alignments>`_. But</span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext">that recipe is *extremely* slow-and-accurate. You can `tune</span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"><last-tuning.html>`_ it to compare huge, high-similarity genomes with</span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">moderate run time and memory use:</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">``fastq-interleave`` ensures that each read has a unique name (by</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">appending "/1" and "/2" if necessary).</span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">* Omit the sensitivity-boosting lastal -m option.</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">Aligning potentially-spliced Illumina reads to a genome</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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200
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"><span class="idiff left right">* Replace ``-uNEAR`` with ``-uRY32``</span>.</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"><span class="idiff left right">See last-split_ (and last-pair-probs_)</span>.</span>
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202
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">* If the "reference" genome (the one given to lastdb) is > 4 GB, it's</span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> probably more efficient to use lastdb8 and lastal8, instead of</span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"> lastdb and lastal.</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">Aligning human & chimp genomes</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">------------------------------</span>
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206
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">Example 10: Ambiguity of alignment columns</span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext">------------------------------------------</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">This is very slow-and-sensitive::</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> lastdb -P8 -uNEAR -R01 humdb human_no_alt_analysis_set.fa</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> last-train -P8 --revsym -E0.05 -C2 humdb chimp.fa > humchi.train</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> lastal -E0.05 -C2 -p humchi.train humdb chimp.fa | last-split > humchi1.maf</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">``--revsym`` makes the substitution rates the same on both strands.</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">For example, it makes A→G equal T→C (because A→G on one strand means</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">T→C on the other strand). This is usually appropriate for</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">genome-genome comparison (but maybe not for mitochondria which have</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">asymmetric "heavy" and "light" strands).</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">``-E0.05`` means only get significant_ alignments that would be</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">expected to occur by chance at a rate ≤ 0.05 times per pair of random</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">sequences of length 1 billion each.</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">The result so far is asymmetric: each part of the chimp genome is</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">aligned to at most one part of the human genome, but not vice-versa.</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">We can get one-to-one alignments like this::</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> maf-swap humchi1.maf | last-split > humchi2.maf</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">Then we can discard less-confident alignments, and convert_ to a</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">compact tabular format::</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> last-postmask humchi2.maf | maf-convert -n tab | awk -F= '$2 <= 1e-5' > humchi.tab</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">last-postmask_ discards alignments caused by simple sequence. The</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">``awk`` command gets alignments with `mismap probability`_ ≤ 10^-5.</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">Finally, we can make a dotplot_::</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> last-dotplot humchi.tab humchi.png</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">To go faster, with minor accuracy loss: replace ``-uNEAR`` with</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">``-uRY32`` and/or `mask repeats`_.</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">To squeeze out the last 0.000...1% of accuracy: add ``-m50`` to the</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">lastal_ options.</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">Aligning human & mouse genomes</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">You can do this in the same way as human/chimp, except that ``-uNEAR``</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">should be omitted. To increase sensitivity, but also time and memory</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">use, add lastdb seeding_ option ``-uMAM4`` or or ``-uMAM8``. To</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">increase them even more, add lastal_ option ``-m100`` (or as high as</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">you can bear).</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">Large reference sequences</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">-------------------------</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">If the sequences that you give to lastdb exceed ~4 billion letters,</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">consider using 8-byte LAST (lastdb8_ and lastal8_). Ordinary (4-byte)</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">LAST can't handle so much sequence at once, so lastdb_ splits it into</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">"volumes", which may be inefficient. 8-byte LAST avoids voluming, but</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">uses more memory. So lastdb8_ works well with a memory-reducing</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">option: ``-uRY`` or ``-w`` or ``-W``.</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">Moar faster</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">-----------</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">* `Using multiple CPUs / cores <last-parallel.html>`_</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">* `Various speed & memory options <last-tuning.html>`_</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">Ambiguity of alignment columns</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">------------------------------</span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="plaintext">Consider this alignment::</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext"></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">@@ -214,13 +337,10 @@ Consider this alignment::</td>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="plaintext"> TGAAGTTAGAGGTAT--GGTTTTGAGTAGT----CCTCCTATTTTTCGAATATCTTG</span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="plaintext">The middle section has such weak similarity that its precise alignment</span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext">cannot be confidently inferred.</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext">It is sometimes useful to estimate the ambiguity of each column in an</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">alignment. We can do that using lastal option -j4::</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">cannot be confidently inferred. We can see the confidence of each</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">alignment column with lastal_ option ``-j4``::</span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext"> lastdb -cR01 humdb humanMito.fa</span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext"> lastal -j4 humdb fuguMito.fa > myalns.maf</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> lastal -j4 -p hufu.train humdb fuguMito.fa > myalns.maf</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">The output looks like this::</span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext"></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">@@ -230,7 +350,7 @@ The output looks like this::</td>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext"> p %*.14442011.(%##"%$$$$###""!!!""""&'(*,340.,,.~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="plaintext">The "p" line indicates the probability that each column is wrongly</span>
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233
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext">aligned, using a compact code (the same as fastq<span class="idiff left right">-sanger</span> format):</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">aligned, using a compact code (the same as fastq<span class="idiff left right">_</span> format):</span>
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234
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext"></span>
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235
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext"> ====== ================= ====== =================</span>
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236
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext"> Symbol Error probability Symbol Error probability</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">@@ -256,5 +376,26 @@ Note that each alignment is grown from a "core" region, and the</td>
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256
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="plaintext">ambiguity estimates assume that the core is correctly aligned. The</span>
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257
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="plaintext">core is indicated by "~" symbols, and it contains exact matches only.</span>
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258
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="plaintext"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">LAST has options to find alignments with optimal column probabilities,</span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">instead of optimal score: see `<lastal.html>`_.</span></pre>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">.. _last: last.html</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">.. _lastdb8:</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">.. _lastdb: lastdb.html</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">.. _lastal8:</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">.. _lastal: lastal.html</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">.. _dotplot: last-dotplot.html</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">.. _last-pair-probs: last-pair-probs.html</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">.. _last-postmask: last-postmask.html</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">.. _mismap probability:</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">.. _last-split: last-split.html</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">.. _last-train: last-train.html</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">.. _convert:</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">.. _maf-convert: maf-convert.html</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">.. _scoring scheme: last-matrices.html</span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">.. _seeding scheme:</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">.. _seeding: last-seeds.html</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">.. _last-evalues:</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">.. _significant:</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">.. _significance: last-evalues.html</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">.. _fastq: https://doi.org/10.1093/nar/gkp1137</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">.. _here:</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">.. _mask repeats: https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">.. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5</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">@@ -318,26 +318,25 @@ table.field-list { border: thin solid green }</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"document"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"last-genome-scale-sequence-comparison"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: #000080;">></span>LAST: Genome-Scale Sequence Comparison<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST finds <span class="idiff left right">similar regions between sequences, and aligns them. It i</span>s</span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html">designed for <span class="idiff left right">comparing large datasets to each other (e.g. vertebrate</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html"><span class="idiff left right">genomes and/or large numbers of DNA reads). It can</span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST finds <span class="idiff left right">and aligns similar regions between sequences. It'</span>s</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="html">designed for <span class="idiff left right">moderately large data (e.g. genomes, DNA reads,</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="html"><span class="idiff left right">proteomes). It's especially good at</span>:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Indicate the (un)ambiguity of each column in an alignment.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Finding sequence rearrangements and recombinations: we believe</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-split.html"</span><span class="nt" style="color: #000080;">></span>last-split<span class="nt" style="color: #000080;"></a></span> does that more rigorously than anything else.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Use sequence quality data in a rigorous fashion.<span class="nt" style="color: #000080;"></p></span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Finding related parts of DNA and proteins, especially protein</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="html">fossils (but introns are not considered).<span class="nt" style="color: #000080;"></p></span></span>
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328
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Align DNA to proteins with frameshifts.<span class="nt" style="color: #000080;"></p></span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Unusual data, e.g. AT-rich DNA, because we can <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>fit<span class="nt" style="color: #000080;"></a></span> parameters to</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="html">the data and calculate <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significance<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Compare PSSMs to sequences.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Calculate the likelihood of chance similarities between random</span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="html">sequences.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Do split and spliced alignment.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Train alignment parameters for unusual kinds of sequence (e.g. nanopore).<span class="nt" style="color: #000080;"></p></span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Sensitive DNA-DNA search, due to <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>fitting<span class="nt" style="color: #000080;"></a></span>, sensitive <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-seeds.html"</span><span class="nt" style="color: #000080;">></span>seeding<span class="nt" style="color: #000080;"></a></span>, and</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="html">calculating <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>significance<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>It can also: indicate the confidence/uncertainty of each column in an</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="html">alignment, and use sequence quality data in a rigorous fashion.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"requirements"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Requirements<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To handle mammalian genomes, it's best if you have at least 10-20</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">@@ -354,17 +353,8 @@ compile the programs, type:</p></td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="html">make</span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You might get some harmless warning messages. If your compiler is</span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="html">really old, you might get an error message like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="html">unrecognized command line option <span class="ni" style="color: #800080;">"</span>-std=c++11<span class="ni" style="color: #800080;">"</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>In that case, you can compile like this (which will disable</span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="html">multi-threading):<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="html">make CXXFLAGS=-O3</span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Or you can specify another compiler like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>You might get some harmless warning messages. It's possible to</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html">specify a C++ compiler like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="html">make CXX=MyOtherCompiler</span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></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">@@ -398,13 +388,9 @@ the new programs.</p></td>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="html">Public License, either version 3 of the License, or (at your option)</span>
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="html">any later version.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"website"</span><span class="nt" style="color: #000080;">></span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Website<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>LAST's website is: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://last.cbrc.jp/"</span><span class="nt" style="color: #000080;">></span>http://last.cbrc.jp/<span class="nt" style="color: #000080;"></a></p></span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"section"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"contact"</span><span class="nt" style="color: #000080;">></span></span>
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406
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span>Contact<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Questions and feedback are <span class="idiff left right">very </span>welcome. We like to use a <span class="nt" style="color: #000080;"><strong></span>public<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Questions and feedback are welcome. We like to use a <span class="nt" style="color: #000080;"><strong></span>public<span class="nt" style="color: #000080;"></strong></span></span>
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408
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="html">mailing list, so everyone can benefit from the discussion:<span class="nt" style="color: #000080;"></p></span></span>
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409
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="html">last-align (ATmark) googlegroups (dot) com<span class="nt" style="color: #000080;"></blockquote></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" 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>
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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">@@ -419,9 +405,6 @@ will never send rude or mocking replies.</p></td>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="html">error, please try to: tell us the LAST version number and exact error</span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="html">message, and give us some input data and exact commands that trigger</span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="html">the problem.<span class="nt" style="color: #000080;"></strong></p></span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you do a benchmarking test of LAST, we recommend you contact us to</span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="html">check you are using it in a suitable way. The history of</span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="html">bioinformatics benchmarks shows it is all too easy to get this wrong.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="html"><span class="nt" style="color: #000080;"></body></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#1eae4cca621ba67dde5fa0a501ceab79fa666725"><strong>doc/last.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">LAST: Genome-Scale Sequence Comparison</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">LAST finds similar regions between sequences, and aligns them. It is</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">designed for comparing large datasets to each other (e.g. vertebrate</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">genomes and/or large numbers of DNA reads). It can:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">* Indicate the (un)ambiguity of each column in an alignment.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">* Use sequence quality data in a rigorous fashion.</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">* Align DNA to proteins with frameshifts.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">* Compare PSSMs to sequences.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">* Calculate the likelihood of chance similarities between random</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> sequences.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">* Do split and spliced alignment.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">* Train alignment parameters for unusual kinds of sequence (e.g. nanopore).</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">LAST finds and aligns similar regions between sequences. It's</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">designed for moderately large data (e.g. genomes, DNA reads,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">proteomes). It's especially good at:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* Finding sequence rearrangements and recombinations: we believe</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> last-split_ does that more rigorously than anything else.</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">* Finding related parts of DNA and proteins, especially protein</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> fossils (but introns are not considered).</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* Unusual data, e.g. AT-rich DNA, because we can fit_ parameters to</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> the data and calculate significance_.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* Sensitive DNA-DNA search, due to fitting_, sensitive seeding_, and</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> calculating significance_.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">It can also: indicate the confidence/uncertainty of each column in an</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">alignment, and use sequence quality data in a rigorous fashion.</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">Requirements</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">------------</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">@@ -33,17 +39,8 @@ compile the programs, type::</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> make</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">You might get some harmless warning messages. If your compiler is</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">really old, you might get an error message like this::</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> unrecognized command line option "-std=c++11"</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">In that case, you can compile like this (which will disable</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">multi-threading)::</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> make CXXFLAGS=-O3</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">Or you can specify another compiler like this::</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">You might get some harmless warning messages. It's possible to</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">specify a C++ compiler like this::</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> make CXX=MyOtherCompiler</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></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">@@ -80,15 +77,10 @@ LAST (including the scripts) is distributed under the GNU General</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">Public License, either version 3 of the License, or (at your option)</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">any later version.</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Website</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">LAST's website is: http://last.cbrc.jp/</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">Contact</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">Questions and feedback are <span class="idiff left right">very </span>welcome. We like to use a **public**</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Questions and feedback are welcome. We like to use a **public**</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">mailing list, so everyone can benefit from the discussion:</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> last-align (ATmark) googlegroups (dot) com</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">@@ -106,6 +98,8 @@ error, please try to: tell us the LAST version number and exact error</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">message, and give us some input data and exact commands that trigger</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">the problem.**</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">If you do a benchmarking test of LAST, we recommend you contact us to</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">check you are using it in a suitable way. The history of</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">bioinformatics benchmarks shows it is all too easy to get this wrong.</span></pre>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">.. _fit:</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.. _fitting: last-train.html</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.. _last-split: last-split.html</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">.. _seeding: last-seeds.html</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.. _significance: last-evalues.html</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">@@ -435,11 +435,13 @@ MAF.</p></td>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-D <span class="nt" style="color: #000080;"><var></span>LENGTH<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Report alignments that are expected by chance at most once per</span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="html">LENGTH query letters. This option only affects the default</span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="html">value of -E, so if you specify -E then -D has no effect.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="html">value of <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-E<span class="nt" style="color: #000080;"></span></tt></span>, so if you specify <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-E<span class="nt" style="color: #000080;"></span></tt></span> then <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-D<span class="nt" style="color: #000080;"></span></tt></span> has no</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="html">effect.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-E <span class="nt" style="color: #000080;"><var></span>THRESHOLD<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Maximum EG2 (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-evalues.html"</span><span class="nt" style="color: #000080;">></span>expected alignments per square giga<span class="nt" style="color: #000080;"></a></span>). This option only affects the default</span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="html">value of -e, so if you specify -e then -E has no effect.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="html">value of <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-e<span class="nt" style="color: #000080;"></span></tt></span>, so if you specify <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-e<span class="nt" style="color: #000080;"></span></tt></span> then <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-E<span class="nt" style="color: #000080;"></span></tt></span> has no</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="html">effect.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="html"><span class="nt" style="color: #000080;"></tbody></span></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">@@ -507,12 +509,19 @@ regions have sizes j and k, where j ≤ k, the cost is: a +</td>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="html">b⋅(k-j) + c⋅j. If c ≥ a + 2b (the default), it reduces to</span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="html">standard affine gaps.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-F <span class="nt" style="color: #000080;"><var></span><span class="idiff left right">CO</span>ST<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-F <span class="nt" style="color: #000080;"><var></span><span class="idiff left right">LI</span>ST<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"><span class="nt" style="color: #000080;"><td><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>Align DNA queries to protein reference sequences, using the</span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="html">specified frameshift cost. A value of 15 seems to be</span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="html">reasonable. (As a special case, -F0 means DNA-versus-protein</span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="html">alignment without frameshifts, which is faster.) The output</span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="html">looks like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="html">specified frameshift cost(s): either one cost (old-style</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="html">frameshifts), or 4 comma-separated costs (new-style</span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="html">frameshifts). As a special case, <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>-F0<span class="nt" style="color: #000080;"></span></tt></span> means</span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="html">DNA-versus-protein alignment without frameshifts, which is</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="html">faster.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The four new-style frameshift costs are for, in order: deletion</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="html">of length k mod 3 = 1 bases, deletion of k mod 3 = 2 bases,</span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="html">insertion of k mod 3 = 1 bases, insertion of k mod 3 = 2 bases.</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="html">(You're expected to get them from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"last-train.html"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></a></span>, not set them</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html">manually.)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The output looks like this:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="html"><span class="nt" style="color: #000080;"><pre</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal-block"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="html">a score=108</span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="html">s prot 2 40 + 649 FLLQAVKLQDP-STPHQIVPSP-VSDLIATHTLCPRMKYQDD</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">@@ -535,12 +544,12 @@ The default value is e-1, which arguably produces the best</td>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="html">alignments. Lower values improve speed, by quitting unpromising</span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="html">extensions sooner. You can specify this parameter in 3 ways:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="html"><span class="nt" style="color: #000080;"><ul</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A score (e.g. <span class="idiff left right">-z20</span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A score (e.g. <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-z20</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span>).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A percentage. For example, <span class="idiff left right">-z50% specifies 50% of the default</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="html">value (rounded down to the nearest integer).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A percentage. For example, <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-z50%</span><span class="nt" style="color: #000080;"><span class="idiff"></span></tt></span></span><span class="idiff right"> specifies 50% of the</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="html"><span class="idiff left right">default </span>value (rounded down to the nearest integer).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A maximum gap length. For example, <span class="idiff left right">-z8g</span> sets the maximum</span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"first"</span><span class="nt" style="color: #000080;">></span>A maximum gap length. For example, <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-z8g</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> sets the maximum</span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="html">score drop to: min[a+8b, A+8B]. However, this never increases</span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="html">the value above the default.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></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">@@ -724,8 +733,10 @@ with the following meanings.</p></td>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>Details: Tantan is applied separately to forward and reverse</span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="html">strands. For DNA-versus-protein alignment (option -F), it is</span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="html">applied to the DNA after translation, at the protein level.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="html">strands. For DNA-versus-protein alignment, if you use a codon</span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="html">substitution matrix (e.g. from <span class="nt" style="color: #000080;"><tt</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"docutils literal"</span><span class="nt" style="color: #000080;">><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>last-train<span class="nt" style="color: #000080;"></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"pre"</span><span class="nt" style="color: #000080;">></span>--codon<span class="nt" style="color: #000080;"></span></tt></span>), tantan</span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="html">is applied to the DNA before translation, else it is applied</span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="html">after translation.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-u <span class="nt" style="color: #000080;"><var></span>NUMBER<span class="nt" style="color: #000080;"></var></span></kbd></td></span></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">@@ -766,14 +777,13 @@ alignment</p></td>
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="html">this core<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>Use <span class="idiff left right">-w0</span> to turn this off.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="html"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"last"</span><span class="nt" style="color: #000080;">></span>Use <span class="nt" style="color: #000080;"><span class="idiff left"><tt</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docutils literal"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"pre"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">-w0</span><span class="nt" style="color: #000080;"><span class="idiff right"></span></tt></span></span> to turn this off.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>-G <span class="nt" style="color: #000080;"><var></span>GENETIC-CODE<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Specify the genetic code for translating DNA to protein. This</span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="html">option has no effect unless DNA-versus-protein alignment is</span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="html">selected with option -F. Codes are specified by numbers</span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="html">(e.g. 1 = standard, 2 = vertebrate mitochondrial), listed here:</span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Specify the genetic code for translating DNA to protein. Codes</span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="html">are specified by numbers (e.g. 1 = standard, 2 = vertebrate</span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="html">mitochondrial), listed here:</span>
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777
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"reference external"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi"</span><span class="nt" style="color: #000080;">></span>https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi<span class="nt" style="color: #000080;"></a></span>. Any</span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="html">other GENETIC-CODE is assumed to be a file name: for an example</span>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="html">of the format, see vertebrateMito.gc in the examples directory.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#30d864ed8925787ee70643db49814772753a5f2c"><strong>doc/lastal.txt</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">@@ -108,12 +108,14 @@ E-value options</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> -D LENGTH</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> Report alignments that are expected by chance at most once per</span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> LENGTH query letters. This option only affects the default</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> value of -E, so if you specify -E then -D has no effect.</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> value of ``-E``, so if you specify ``-E`` then ``-D`` has no</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> effect.</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> -E THRESHOLD</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> Maximum EG2 (`expected alignments per square giga</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> <last-evalues.html>`_). This option only affects the default</span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> value of -e, so if you specify -e then -E has no effect.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> value of ``-e``, so if you specify ``-e`` then ``-E`` has no</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> effect.</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">Score options</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">~~~~~~~~~~~~~</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">@@ -175,12 +177,21 @@ Score options</td>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> b⋅(k-j) + c⋅j. If c ≥ a + 2b (the default), it reduces to</span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"> standard affine gaps.</span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> -F <span class="idiff left right">CO</span>ST</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> -F <span class="idiff left right">LI</span>ST</span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"> Align DNA queries to protein reference sequences, using the</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> specified frameshift cost. A value of 15 seems to be</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> reasonable. (As a special case, -F0 means DNA-versus-protein</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> alignment without frameshifts, which is faster.) The output</span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> looks like this::</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> specified frameshift cost(s): either one cost (old-style</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> frameshifts), or 4 comma-separated costs (new-style</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> frameshifts). As a special case, ``-F0`` means</span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> DNA-versus-protein alignment without frameshifts, which is</span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> faster.</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> The four new-style frameshift costs are for, in order: deletion</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> of length k mod 3 = 1 bases, deletion of k mod 3 = 2 bases,</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> insertion of k mod 3 = 1 bases, insertion of k mod 3 = 2 bases.</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> (You're expected to get them from last-train_, not set them</span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> manually.)</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> The output looks like this::</span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext"> a score=108</span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="plaintext"> s prot 2 40 + 649 FLLQAVKLQDP-STPHQIVPSP-VSDLIATHTLCPRMKYQDD</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">@@ -202,12 +213,12 @@ Score options</td>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext"> alignments. Lower values improve speed, by quitting unpromising</span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext"> extensions sooner. You can specify this parameter in 3 ways:</span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"> * A score (e.g. <span class="idiff left right">-z20</span>).</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> * A score (e.g. <span class="idiff left right">``-z20``</span>).</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext"> * A percentage. For example, <span class="idiff left right">-z50% specifies 50% of the default</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"> value (rounded down to the nearest integer).</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> * A percentage. For example, <span class="idiff left right">``-z50%`` specifies 50% of the</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> <span class="idiff left right">default </span>value (rounded down to the nearest integer).</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"> * A maximum gap length. For example, <span class="idiff left right">-z8g</span> sets the maximum</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> * A maximum gap length. For example, <span class="idiff left right">``-z8g``</span> sets the maximum</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"> score drop to: min[a+8b, A+8B]. However, this never increases</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext"> the value above the default.</span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext"></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">@@ -361,8 +372,10 @@ Miscellaneous options</td>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="plaintext"> 2. Convert simple repeats, within AT-rich DNA, to lowercase.</span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="plaintext"> Details: Tantan is applied separately to forward and reverse</span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="plaintext"> strands. For DNA-versus-protein alignment (option -F), it is</span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="plaintext"> applied to the DNA after translation, at the protein level.</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> strands. For DNA-versus-protein alignment, if you use a codon</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> substitution matrix (e.g. from ``last-train --codon``), tantan</span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> is applied to the DNA before translation, else it is applied</span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> after translation.</span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="plaintext"> -u NUMBER</span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="plaintext"> Specify treatment of lowercase letters when extending</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">@@ -398,13 +411,12 @@ Miscellaneous options</td>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="plaintext"> * has start coordinates offset by DISTANCE or less relative to</span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="plaintext"> this core</span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="plaintext"> Use <span class="idiff left right">-w0</span> to turn this off.</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> Use <span class="idiff left right">``-w0``</span> to turn this off.</span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="plaintext"> -G GENETIC-CODE</span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="plaintext"> Specify the genetic code for translating DNA to protein. This</span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="plaintext"> option has no effect unless DNA-versus-protein alignment is</span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="plaintext"> selected with option -F. Codes are specified by numbers</span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="plaintext"> (e.g. 1 = standard, 2 = vertebrate mitochondrial), listed here:</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> Specify the genetic code for translating DNA to protein. Codes</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> are specified by numbers (e.g. 1 = standard, 2 = vertebrate</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> mitochondrial), listed here:</span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext"> https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. Any</span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="plaintext"> other GENETIC-CODE is assumed to be a file name: for an example</span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext"> of the format, see vertebrateMito.gc in the examples directory.</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">@@ -588,3 +600,5 @@ lastal8</td>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="plaintext">lastal8 has identical usage to lastal, and is used with `lastdb8</span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="plaintext"><lastdb.html>`_. lastal cannot read the output of lastdb8, and</span>
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="plaintext">lastal8 cannot read the output of lastdb.</span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext">.. _last-train: last-train.html</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</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">@@ -19,6 +19,7 @@ import sys</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">proteinAlphabet20</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACDEFGHIKLMNPQRSTVWY"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">proteinAlphabet21</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinAlphabet20</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"*"</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># faster than fileinput</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></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">@@ -183,7 +184,7 @@ def scaleFromHeader(lines):</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"couldn't read the scale"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">nTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">nTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">9</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">codon</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">5</span></span>
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187
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nTransitions</span> <span class="c1" style="color: #998; font-style: italic;"># +1 pseudocounts</span></span>
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188
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># deletes: opens + extensions, so 2 pseudocounts</span></span>
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189
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">tranCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span> <span class="c1" style="color: #998; font-style: italic;"># inserts: opens + extensions, so 2 pseudocounts</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" 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="197" 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">@@ -196,13 +197,15 @@ def countsFromLastOutput(lines, opts):</td>
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196
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">:]]</span></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">countMatrix</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nTransitions</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">nCols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">nCols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">64</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">codon</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">matrixSize</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">nRows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">nCols</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">countMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nCols</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nCols</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">alignmentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">pseudocount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">countMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">pseudocount</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nCols</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nCols</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">alignmentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">matrixSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">identities</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nRows</span><span class="p">):</span></span>
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207
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nCols</span><span class="p">):</span></span>
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208
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" 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="217" 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">@@ -214,6 +217,13 @@ def countsFromLastOutput(lines, opts):</td>
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214
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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215
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span></span>
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216
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"no alignments"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">pseudocounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nRows</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">32</span> <span class="c1" style="color: #998; font-style: italic;"># xxx ???</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">rowSums</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">countMatrix</span><span class="p">]</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">colSums</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">countMatrix</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">mul</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pseudocounts</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">rowSums</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">colSums</span><span class="p">))</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">countMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mul</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">j</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">colSums</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">rowSums</span><span class="p">,</span> <span class="n" style="color: #333;">countMatrix</span><span class="p">)]</span></span>
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217
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">countMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">alignments</span><span class="p">]</span></span>
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218
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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219
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scoreFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">prob</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="414" 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="424" 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">@@ -414,21 +424,260 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):</td>
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414
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="s" style="color: #d14;">"doubling the scale"</span><span class="p">)</span></span>
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415
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">originalScale</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">isLastFormat</span><span class="p">,</span> <span class="n" style="color: #333;">outFile</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">delInit</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">insInit</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrow</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrow</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### Routines for codons & frameshifts:</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialCodonSubstitutionProbs</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">b1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">b3</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">61</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">19</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"initial match probability must be < 61/64"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">q</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aa</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">proteinAlphabet20</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="n" style="color: #333;">b3</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">codon</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"*"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matrix</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">codon</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">proteinAlphabet20</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)][</span><span class="n" style="color: #333;">codon</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matrix</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialCodonProbs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initialCodonSubstitutionProbs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">delGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">insGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.99</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insOpenProb</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">F</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">delProb1</span><span class="p">,</span> <span class="n" style="color: #333;">delProb2</span><span class="p">,</span> <span class="n" style="color: #333;">insProb1</span><span class="p">,</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">F</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrowProb</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrowProb</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">delProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProb1</span><span class="p">,</span> <span class="n" style="color: #333;">delProb2</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">insProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">insProb1</span><span class="p">,</span> <span class="n" style="color: #333;">insProb2</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">formattedCodons</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"acgt"</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printCodonCountMatrix</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">formattedCodons</span><span class="p">(</span><span class="s" style="color: #d14;">"5"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">proteinAlphabet21</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"<5.4g"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeCodonScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span><span class="p">,</span> <span class="n" style="color: #333;">matrixAndProbs</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrixAndProbs</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">maxLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matrix</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">maxLen</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">formattedCodons</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">proteinAlphabet21</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colProbs</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">codonMatProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">probs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# count matrix "</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">printCodonCountMatrix</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">probs</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">freqText</span><span class="p">(</span><span class="n" style="color: #333;">probability</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">probability</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">".2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"<3.2g"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftProbImbalance</span><span class="p">(</span><span class="n" style="color: #333;">endProb</span><span class="p">,</span> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">ins1</span><span class="p">,</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insProbs</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">del1</span><span class="p">,</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delProbs</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">iNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">ins1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">iDen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insGrowProb</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">dNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">del1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">dDen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delGrowProb</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iNum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">iDen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dNum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">dDen</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">balancedFrameshiftEndProb</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">ins1</span><span class="p">,</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insProbs</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">del1</span><span class="p">,</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delProbs</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">((</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">frameshiftProbImbalance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">deletes</span><span class="p">,</span> <span class="n" style="color: #333;">inserts</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens0</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">delOpens1</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens2</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens1</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens2</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens2</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpens0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens2</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python"> <span class="n" style="color: #333;">denominator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">insGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insOpens0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">inserts</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpens2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens2</span><span class="p">)</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpens1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">inserts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens1</span><span class="p">)</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denominator</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">delGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delOpens0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">deletes</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens2</span><span class="p">)</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delOpens1</span><span class="p">)</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# aligned residue/codon pairs: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# whole codon deletes: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">deletes</span><span class="p">)</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# whole codon inserts: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">inserts</span><span class="p">)</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delOpens: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">delOpens</span><span class="p">)</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insOpens: %.12g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">insOpens</span><span class="p">)</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# frameshifts del-1,del-2,ins+1,ins+2: %.12g,%.12g,%.12g,%.12g"</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">delOpens1</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens2</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens1</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens2</span><span class="p">))</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# alignments:"</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">)</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# matchProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">matchProb</span><span class="p">)</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delOpenProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">)</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insOpenProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">)</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">)</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# frameshiftProbs del-1,del-2,ins+1,ins+2: %g,%g,%g,%g"</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">delProb1</span><span class="p">,</span> <span class="n" style="color: #333;">delProb2</span><span class="p">,</span> <span class="n" style="color: #333;">insProb1</span><span class="p">,</span> <span class="n" style="color: #333;">insProb2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">delProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProb1</span><span class="p">,</span> <span class="n" style="color: #333;">delProb2</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">insProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">insProb1</span><span class="p">,</span> <span class="n" style="color: #333;">insProb2</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftRatiosFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">del1</span><span class="p">,</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delProbs</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">ins1</span><span class="p">,</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insProbs</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedFrameshiftEndProb</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">6</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">insAdj</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">insGrowProb</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">insOpenRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insAdj</span></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">insMean</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">insRatio0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insMean</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">insRatio1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ins1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">insAdj</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insMean</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">insRatio2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ins1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">insAdj</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insMean</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insOpenRatio</span><span class="p">,</span> <span class="n" style="color: #333;">insRatio0</span><span class="p">,</span> <span class="n" style="color: #333;">insRatio1</span><span class="p">,</span> <span class="n" style="color: #333;">insRatio2</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">delAdj</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">delGrowProb</span></span>
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">delOpenRatio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delAdj</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">delMean</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">delRatio0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delMean</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">endProb</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">delRatio1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">del1</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">delAdj</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delMean</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">endProb</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">delRatio2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">del1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">delAdj</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">delMean</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">endProb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">delRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpenRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatio0</span><span class="p">,</span> <span class="n" style="color: #333;">delRatio1</span><span class="p">,</span> <span class="n" style="color: #333;">delRatio2</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatios</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">gapOpenRatio</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio0</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio1</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatios</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">gapOpenCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapOpenRatio</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">gapCost0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio0</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">gapCost1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">gapCost2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapRatio2</span><span class="p">)</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gapOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost0</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost1</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost2</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftImbalanceFromGap</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">):</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="n" style="color: #333;">gapOpenCost</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost0</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost1</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapOpenCost</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapCost0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapCost1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapCost2</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">frameshiftScoreImbalance</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span><span class="p">,</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">):</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftImbalanceFromGap</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">)</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftImbalanceFromGap</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">)</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">matScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">rowProbs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">colProbs</span><span class="p">))</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">normalizedFreqs</span><span class="p">(</span><span class="n" style="color: #333;">freqs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">freqs</span><span class="p">))</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">codonScoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">):</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowFreqs</span><span class="p">,</span> <span class="n" style="color: #333;">colFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matParams</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalizedFreqs</span><span class="p">(</span><span class="n" style="color: #333;">rowFreqs</span><span class="p">)</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalizedFreqs</span><span class="p">(</span><span class="n" style="color: #333;">colFreqs</span><span class="p">)</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">matParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matParams</span><span class="p">)</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">)</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">insCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">frameshiftScoreImbalance</span><span class="p">,</span> <span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># XXX</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">rowFreqs</span><span class="p">,</span> <span class="n" style="color: #333;">colFreqs</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isCloseEnough</span><span class="p">(</span><span class="n" style="color: #333;">oldParameters</span><span class="p">,</span> <span class="n" style="color: #333;">newParameters</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python"> <span class="n" style="color: #333;">delCosts0</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts0</span><span class="p">,</span> <span class="n" style="color: #333;">substitutionParameters0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldParameters</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">m0</span><span class="p">,</span> <span class="n" style="color: #333;">rowFreqs0</span><span class="p">,</span> <span class="n" style="color: #333;">colFreqs0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionParameters0</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">delCosts1</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts1</span><span class="p">,</span> <span class="n" style="color: #333;">substitutionParameters1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newParameters</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">m1</span><span class="p">,</span> <span class="n" style="color: #333;">rowFreqs1</span><span class="p">,</span> <span class="n" style="color: #333;">colFreqs1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionParameters1</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">delCosts0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">delCosts1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">insCosts0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">insCosts1</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">m0</span><span class="p">,</span> <span class="n" style="color: #333;">m1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### End of routines for codons & frameshifts</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">isLastFormat</span><span class="p">,</span> <span class="n" style="color: #333;">outFile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span><span class="p">,</span> <span class="n" style="color: #333;">del1</span><span class="p">,</span> <span class="n" style="color: #333;">del2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span><span class="p">,</span> <span class="n" style="color: #333;">ins1</span><span class="p">,</span> <span class="n" style="color: #333;">ins2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python"> <span class="n" style="color: #333;">frameshiftCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">del1</span><span class="p">,</span> <span class="n" style="color: #333;">del2</span><span class="p">,</span> <span class="n" style="color: #333;">ins1</span><span class="p">,</span> <span class="n" style="color: #333;">ins2</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">frameshiftCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">))</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="n" style="color: #333;">delInit</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">insInit</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">delOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delGrow</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">insOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insGrow</span></span>
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422
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isLastFormat</span><span class="p">:</span></span>
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423
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -a"</span><span class="p">,</span> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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424
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -A"</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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425
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -b"</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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426
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -B"</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -F"</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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427
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">delOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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429
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExistCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">insOpen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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430
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">delGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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431
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendCost:"</span><span class="p">,</span> <span class="n" style="color: #333;">insGrow</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# frameshiftCosts del-1,del-2,ins+1,ins+2:"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">)</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codonMatProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span></span>
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"></span>
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433
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tryToMakeChildProgramsFindable</span><span class="p">():</span></span>
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434
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="458" 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>
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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">@@ -458,6 +707,8 @@ def fixedLastalArgs(opts, lastalProgName):</td>
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458
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-X"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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459
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-Q"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">)</span></span>
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460
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"v"</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-K1"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">inStream</span><span class="p">):</span></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">@@ -480,78 +731,97 @@ def lastSplitProcess(opts, proc):</td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doTraining</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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481
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="python"> <span class="n" style="color: #333;">tryToMakeChildProgramsFindable</span><span class="p">()</span></span>
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482
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python"> <span class="n" style="color: #333;">lastalProgName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readLastalProgName</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">scaleIncrease</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span> <span class="c1" style="color: #998; font-style: italic;"># while training, up-scale the scores by this amount</span></span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">lastalVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionFromLastal</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# lastal version:"</span><span class="p">,</span> <span class="n" style="color: #333;">lastalVersion</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="n" style="color: #333;">scaleIncrease</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">gapRatiosFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftRatiosFromProbs</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">scoresAndScaleFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codonScoresAndScale</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrixFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeCodonScoreMatrix</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="n" style="color: #333;">scaleIncrease</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span> <span class="c1" style="color: #998; font-style: italic;"># while training, upscale the scores by this amount</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python"> <span class="n" style="color: #333;">gapRatiosFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatiosFromProbs</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="python"> <span class="n" style="color: #333;">scoresAndScaleFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScale</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrixFunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeScoreMatrix</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedLastalArgs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalProgName</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-p"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-a"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-A"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# maximum percent identity:"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span><span class="p">)</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedLastalArgs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalProgName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">)</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-p"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-a"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-A"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">)</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">)</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span><span class="p">:</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaleFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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497
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python"></span>
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498
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span><span class="p">:</span></span>
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499
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="python"> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaleFromHeader</span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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502
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"></span>
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503
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python"> <span class="n" style="color: #333;">internalScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">externalScale</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaleIncrease</span></span>
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504
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="n" style="color: #333;">oldParameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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505
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="python"></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# lastal version:"</span><span class="p">,</span> <span class="n" style="color: #333;">lastalVersion</span><span class="p">)</span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# maximum percent identity:"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">pid</span><span class="p">)</span></span>
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508
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# scale of score parameters:"</span><span class="p">,</span> <span class="n" style="color: #333;">externalScale</span><span class="p">)</span></span>
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509
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# scale used while training:"</span><span class="p">,</span> <span class="n" style="color: #333;">internalScale</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initialCodonProbs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">gapCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countsFromLastOutput</span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatiosFromProbs</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gapProbs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatiosFunc</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gapProbs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matProbs</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matProbs</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">freqText</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">freqText</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colProbs</span><span class="p">]</span></span>
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522
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"> <span class="n" style="color: #333;">matParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">as</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scoresAndScale</span></span><span class="p">(</span><span class="n" style="color: #333;">internalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s<span class="idiff left right">a</span>s</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scoresAndScaleFunc</span></span><span class="p">(</span><span class="n" style="color: #333;">internalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ss</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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526
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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527
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>
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528
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix<span class="idiff left right">Func</span></span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">"# "</span><span class="p">)</span></span>
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530
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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531
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parameters</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oldParameters</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">isCloseEnough</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oldParameters</span><span class="p">):</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parameters</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oldParameters</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">oldParameters</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedLastalArgs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalProgName</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-t{0:.6}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-p-"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"> <span class="n" style="color: #333;">lastalArgs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">args</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix<span class="idiff left right">Func</span></span><span class="p">(</span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">as</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scoresAndScale</span></span><span class="p">(</span><span class="n" style="color: #333;">externalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s<span class="idiff left right">a</span>s</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scoresAndScaleFunc</span></span><span class="p">(</span><span class="n" style="color: #333;">externalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ss</span></span>
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -X"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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547
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -Q"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span><span class="p">)</span></span>
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548
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -t{0:.6}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">))</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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550
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -s"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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551
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -S"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span><span class="p">)</span></span>
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552
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# score matrix "</span></span>
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553
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"> <span class="s" style="color: #d14;">"(query letters = columns, reference letters = rows):"</span><span class="p">)</span></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">writeScoreMatrix<span class="idiff left right">Func</span></span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="python"></span>
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556
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lastTrain</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">sample_number</span><span class="p">:</span></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">@@ -586,12 +856,15 @@ if __name__ == "__main__":</td>
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python"> <span class="s" style="color: #d14;">"skip alignments with > PID% identity (default: %default)"</span><span class="p">)</span></span>
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587
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--postmask"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NUMBER"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span></span>
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588
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<td class="diff-line-num new_line" data-linenumber="858" 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">
858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"> <span class="s" style="color: #d14;">"skip mostly-lowercase alignments (default=%default)"</span><span class="p">)</span></span>
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589
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<td class="diff-line-num new_line old" data-linenumber="859" 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="LC589" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-number"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"N"</span><span class="p">,</span></span>
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590
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<td class="diff-line-num new_line old" data-linenumber="859" 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="LC590" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of random sequence samples (default: %default)"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="859" 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">
859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-number"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"N"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="860" 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">
860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of random sequence samples "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="861" 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">
861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="s" style="color: #d14;">"(default: 20000 if --codon else 500)"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="591" 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">
591
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<td class="diff-line-num new_line" data-linenumber="862" 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">
862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample-length"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2000</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"L"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="592" 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">
592
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<td class="diff-line-num new_line" data-linenumber="863" 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">
863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"length of each sample (default: %default)"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="593" 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">
593
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<td class="diff-line-num new_line" data-linenumber="864" 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">
864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--scale"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"float"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"S"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="594" 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">
594
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<td class="diff-line-num new_line" data-linenumber="865" 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">
865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output scores in units of 1/S bits"</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="595" 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="866" 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">
866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--codon"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="595" 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="867" 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">
867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"DNA queries & protein reference, with frameshifts"</span><span class="p">)</span></span>
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595
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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596
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"></span>
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597
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Initial parameter options"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" 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="879" 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">@@ -606,6 +879,8 @@ if __name__ == "__main__":</td>
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606
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gap extension cost (default: 9 if Q>=1, else 3)"</span><span class="p">)</span></span>
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607
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-A"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion existence cost"</span><span class="p">)</span></span>
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608
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<td class="diff-line-num new_line" data-linenumber="881" 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">
881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-B"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"insertion extension cost"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="882" 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">
882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-F"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"LIST"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"frameshift probabilities: "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="883" 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">
883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="s" style="color: #d14;">"del-1,del-2,ins+1,ins+2 (default: 1-b,1-b,1-B,1-B)"</span><span class="p">)</span></span>
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609
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<td class="diff-line-num new_line" data-linenumber="884" 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">
884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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610
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<td class="diff-line-num new_line" data-linenumber="885" 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">
885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="611" 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">
611
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<td class="diff-line-num new_line" data-linenumber="886" 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">
886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment options"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="638" 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="913" 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">@@ -638,8 +913,18 @@ if __name__ == "__main__":</td>
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638
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<td class="diff-line-num new_line" data-linenumber="913" 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">
913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="639" 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">
639
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<td class="diff-line-num new_line" data-linenumber="914" 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">
914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="640" 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">
640
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<td class="diff-line-num new_line" data-linenumber="915" 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">
915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"I need a lastdb index and query sequences"</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="641" 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="916" 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">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">sample_number</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="641" 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="917" 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">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">sample_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20000</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">500</span></span>
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<td class="diff-line-num old_line" data-linenumber="641" 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">
641
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<td class="diff-line-num new_line" data-linenumber="918" 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">
918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">sample_number</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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642
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<td class="diff-line-num new_line" data-linenumber="919" 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">
919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"sorry, can't use stdin when --sample-number=0"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" 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">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" 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">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span></span>
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<td class="diff-line-num new old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="922" 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">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.4"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="923" 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">
923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.02"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="924" 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">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.5"</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">a</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">B</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">b</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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643
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">Q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fastx"</span><span class="p">,</span> <span class="s" style="color: #d14;">"keep"</span><span class="p">)):</span></span>
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644
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5"</span></span>
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645
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span><span class="p">:</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5"</span></span>
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<li id="5e55dbeefff2057b414960d9467d183920e31b8a">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#5e55dbeefff2057b414960d9467d183920e31b8a"><strong>src/Alignment.cc</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">@@ -50,7 +50,7 @@ void Alignment::makeXdrop( Aligners &aligners, bool isGreedy,</td>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qual1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qual2</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">AlignmentExtras</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">extras</span><span class="p">,</span></span>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputType</span> <span class="p">){</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">score</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seed</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">probMatrix</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seed</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// else keep the old score</span></span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span> <span class="p">){</span></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">@@ -62,6 +62,7 @@ void Alignment::makeXdrop( Aligners &aligners, bool isGreedy,</td>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// extend a gapped alignment in the left/reverse direction from the seed:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">blocks</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">extend</span><span class="p">(</span> <span class="n" style="color: #333;">blocks</span><span class="p">,</span> <span class="n" style="color: #333;">columnAmbiguityCodes</span><span class="p">,</span> <span class="n" style="color: #333;">aligners</span><span class="p">,</span> <span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg1</span><span class="p">(),</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">beg2</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" 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="311" 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">@@ -310,23 +311,25 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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310
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">getNextChunkFrame</span><span class="p">(</span><span class="n" style="color: #333;">end1</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">))</span></span>
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311
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SegmentPair</span><span class="p">(</span><span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">end2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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312
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">gapCost</span><span class="p">));</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftAligner</span><span class="p">;</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probDropLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">forward</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">getColumnCodes</span><span class="p">(</span><span class="n" style="color: #333;">fxa</span><span class="p">,</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span> <span class="n" style="color: #333;">chunks</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">probMat</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">FrameshiftXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">frameshiftAligner</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probDropLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxDrop</span><span class="p">);</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">forward</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame1</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dnaToAa</span><span class="p">(</span><span class="n" style="color: #333;">frame2</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">),</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="323" 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">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="324" 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">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">getColumnCodes</span><span class="p">(</span><span class="n" style="color: #333;">fxa</span><span class="p">,</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span> <span class="n" style="color: #333;">chunks</span><span class="p">);</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</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">@@ -146,7 +146,7 @@ Score options (default settings):\n\</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"><span class="s" style="color: #d14;">-A: insertion existence cost (a)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="s" style="color: #d14;">-B: insertion extension cost (b)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="s" style="color: #d14;">-c: unaligned residue pair cost (off)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"><span class="s" style="color: #d14;">-F: frameshift cost (off)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"><span class="s" style="color: #d14;">-F: frameshift cost<span class="idiff left right">(s)</span> (off)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"><span class="s" style="color: #d14;">-x: maximum score drop for preliminary gapped alignments (z)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="s" style="color: #d14;">-y: maximum score drop for gapless alignments (min[t*10, x])</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"><span class="s" style="color: #d14;">-z: maximum score drop for final gapped alignments (e-1)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/d1b788bbe87c1e5812ec649f0952e53a399c2fc9#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</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">@@ -458,7 +458,7 @@ static const ScoreMatrixRow *getQueryPssm(const LastAligner &aligner,</td>
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458
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">qualityPssm</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">Phase</span><span class="p">{</span> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">Enum</span><span class="p">{</span> <span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">gapped</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">final</span></span> <span class="p">};</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">Phase</span><span class="p">{</span> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">Enum</span><span class="p">{</span> <span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">pregapped</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gapped</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">postgapped</span></span> <span class="p">};</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isFullScoreThreshold</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">();</span></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">@@ -466,7 +466,7 @@ static bool isFullScoreThreshold() {</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"></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">@@ -493,7 +493,7 @@ struct Dispatcher{</td>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span><span class="p">(</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">ratiosMasked</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">ratios</span> <span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">(</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">twoQualMasked</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">twoQual</span> <span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapless</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapless</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapped</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">pre</span>gapped</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span><span class="p">(</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span> <span class="p">){}</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gaplessOverlap</span><span class="p">(</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">indexT</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fwd</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></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">@@ -637,10 +637,9 @@ void alignGapless1(LastAligner &aligner, SegmentPairPot &gaplessAlns,</td>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Find query matches to the suffix array, and do gapless extensions</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignGapless</span><span class="p">(</span> <span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">SegmentPairPot</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">querySeq</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignGapless</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">SegmentPairPot</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Dispatcher</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dis</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="cpp"> <span class="n" style="color: #333;">DiagonalTable</span> <span class="n" style="color: #333;">dt</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// record already-covered positions on each diagonal</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">maxAlignments</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxAlignmentsPerQueryStrand</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxAlignmentsPerQueryStrand</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></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">@@ -713,9 +712,8 @@ void shrinkToLongestIdenticalRun( SegmentPair& sp, const Dispatcher& dis ){</td>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignGapped</span><span class="p">(</span> <span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentPot</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">SegmentPairPot</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">phase</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span> <span class="n" style="color: #333;">phase</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis</span><span class="p">(</span><span class="n" style="color: #333;">phase</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padLen</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">countT</span> <span class="n" style="color: #333;">gappedExtensionCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlignmentCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Redo the gapless extensions, using gapped score parameters.</span></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">@@ -755,11 +753,10 @@ void alignGapped( LastAligner& aligner,</td>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="n" style="color: #333;">shrinkToLongestIdenticalRun</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do gapped extension from each end of the seed:</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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763
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gappedExtensionCount</span><span class="p">;</span></span>
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"></span>
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minScoreGapped</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="775" 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="772" 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">@@ -775,7 +772,7 @@ void alignGapped( LastAligner& aligner,</td>
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775
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">.</span><span class="n" style="color: #333;">markAllOverlaps</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">blocks</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">.</span><span class="n" style="color: #333;">markTandemRepeats</span><span class="p">(</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxRepeatDistance</span> <span class="p">);</span></span>
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777
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"></span>
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778
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">phase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Phase</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="k" style="font-weight: 600;"><span class="idiff">final</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">phase</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Phase</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">gapped</span></span><span class="p">)</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">);</span></span>
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">SegmentPairPot</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">markAsGood</span><span class="p">(</span><span class="n" style="color: #333;">sp</span><span class="p">);</span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="cpp"></span>
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gappedAlignmentCount</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="786" 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="783" 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">@@ -786,15 +783,26 @@ void alignGapped( LastAligner& aligner,</td>
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786
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG2</span><span class="p">(</span> <span class="s" style="color: #d14;">"gapped alignments="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gappedAlignmentCount</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"><span class="p">}</span></span>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Redo gapped extensions, but keep the old alignment scores</span></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignPostgapped</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">AlignmentPot</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Dispatcher</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dis</span><span class="p">)</span> <span class="p">{</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentExtras</span> <span class="n" style="color: #333;">extras</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// not used</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Print the gapped alignments, after optionally calculating match</span></span>
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// probabilities and re-aligning using the gamma-centroid algorithm</span></span>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignFinish</span><span class="p">(</span> <span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlignmentPot</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span></span>
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dispatcher</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">dis</span></span> <span class="p">){</span></span>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="cpp"> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">centroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">.</span><span class="n" style="color: #333;">centroid</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">final</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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796
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padLen</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>
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797
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">queryLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp"></span>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="p">){</span></span>
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="819" 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>
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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">@@ -819,28 +827,26 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>
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819
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentExtras</span> <span class="n" style="color: #333;">extras</span><span class="p">;</span></span>
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820
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// score is fullScore</span></span>
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821
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span> <span class="p">){</span></span>
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822
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">querySeq</span></span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">b</span></span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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823
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// calculate match probabilities:</span></span>
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824
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">probAln</span><span class="p">;</span></span>
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825
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">;</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">globality</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">m</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alph</span></span><span class="p">,</span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">extras</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span><span class="p">);</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="p"><span class="idiff right">,</span></span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">globality</span></span><span class="p">,</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">minScore</span><span class="p">,</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="838" 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">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dis</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alph</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">extras</span></span><span class="p">,</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span><span class="p">);</span></span>
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832
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<td class="diff-line-num new_line" data-linenumber="840" 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">
840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INF</span><span class="p">);</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">probAln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="843" 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">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">probAln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">eraseWeakAlignments</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">AlignmentPot</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padLen</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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843
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">eraseWeakAlignments</span><span class="p">(</span><span class="n" style="color: #333;">AlignmentPot</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Dispatcher</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dis</span><span class="p">)</span> <span class="p">{</span></span>
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844
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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845
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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846
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">hasGoodSegment</span><span class="p">(</span><span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">minScoreGapped</span><span class="p">),</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="957" 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>
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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">@@ -957,32 +963,38 @@ void scan(LastAligner& aligner, size_t queryNum,</td>
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</span><span class="p">;</span></span>
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958
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964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="cpp"> <span class="n" style="color: #333;">makeQualityPssm</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis0</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapless</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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960
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">SegmentPairPot</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">;</span></span>
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961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapless</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span><span class="p">);</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapless</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dis0</span></span><span class="p">);</span></span>
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962
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// we just want gapless alignments</span></span>
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<td class="diff-line-num old_line" data-linenumber="963" 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">
963
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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964
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="cpp"></span>
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965
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">()))</span></span>
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966
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">unmaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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967
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="968" 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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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">frameSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isFrameshift</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padLen</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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968
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentPot</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">;</span></span>
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969
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="cpp"></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span></span>
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<td class="diff-line-num old old_line" data-linenumber="971" 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">
971
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<td class="diff-line-num new_line old" data-linenumber="978" 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="LC971" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">()))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="972" 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">
972
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<td class="diff-line-num new_line old" data-linenumber="978" 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="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="973" 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">
973
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<td class="diff-line-num new_line old" data-linenumber="978" 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="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapped</span> <span class="p">);</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropFinal</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maxDropGapped</span><span class="p">)</span> <span class="p">{</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pregapped</span><span class="p">);</span></span>
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974
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="cpp"> <span class="n" style="color: #333;">erase_if</span><span class="p">(</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">SegmentPairPot</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isNotMarkedAsGood</span> <span class="p">);</span></span>
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975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">unmaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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977
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="cpp"> <span class="p">}</span></span>
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978
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp"></span>
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979
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<td class="diff-line-num new_line old" data-linenumber="984" 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="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span><span class="idiff left right"> </span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Phase</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="k" style="font-weight: 600;"><span class="idiff">final</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="n" style="color: #333;">alignGapped</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">gaplessAlns</span><span class="p">,</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Phase</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">gapped</span></span><span class="p">);</span></span>
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981
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986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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982
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp"></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dis3</span><span class="p">(</span><span class="n" style="color: #333;">Phase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">postgapped</span><span class="p">,</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span> <span class="p">{</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="cpp"> <span class="n" style="color: #333;">unmaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">alignPostgapped</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">dis3</span><span class="p">);</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="cpp"> <span class="p">}</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"></span>
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983
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995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span> <span class="p">{</span></span>
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"> <span class="n" style="color: #333;">remaskLowercase</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">);</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;">eraseWeakAlignments</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gappedAlns</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matrices</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querySeq</span></span><span class="p">);</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">eraseWeakAlignments</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">gappedAlns</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dis0</span></span><span class="p">);</span></span>
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986
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998
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG2</span><span class="p">(</span><span class="s" style="color: #d14;">"lowercase-filtered alignments="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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987
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999
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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988
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="995" 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="1007" 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">@@ -995,7 +1007,7 @@ void scan(LastAligner& aligner, size_t queryNum,</td>
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995
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp"> <span class="p">}</span></span>
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996
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"></span>
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997
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isCollatedAlignments</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// sort by score</span></span>
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998
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="cpp"> <span class="n" style="color: #333;">alignFinish</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">querySeq</span></span><span class="p">);</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">alignFinish</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">frameSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dis3</span></span><span class="p">);</span></span>
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999
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"><span class="p">}</span></span>
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1000
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp"></span>
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1001
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tantanMaskOneQuery</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"117<span class="idiff left right">0</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"117<span class="idiff left right">8</span>"</span></span></pre>
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