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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/spades">Debian Med / spades</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/2dd0d58b8f01d2914d2d134c21123ade6d05f28b">2dd0d58b</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-11-18T13:21:18Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lots of more python to python3 conversions
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
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<li class="file-stats">
<a href="#6b4e31cdf8f9338db47a4fa236a08014b3851935">
debian/patches/yaml_load.patch
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<h4>Changes:</h4>
<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/spades/commit/2dd0d58b8f01d2914d2d134c21123ade6d05f28b#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" 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">@@ -58,6 +58,18 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -52,9 +52,9 @@</span> def reads_line(libs):</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> def command_line(barcode, output_dir, params, continue_launch):</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> # logfile = os.path.join(output_dir, "logs", barcode.id + ".out")</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> if continue_launch and os.path.exists(os.path.join(output_dir, barcode.id, "params.txt")):</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ["python " + os.path.join(spades_home, "spades.py"), "--truseq", "-o", os.path.join(output_dir, barcode.id), "--continue", params]</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result = ["python3 " + os.path.join(spades_home, "spades.py"), "--truseq", "-o", os.path.join(output_dir, barcode.id), "--continue", params]</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ["python " + os.path.join(spades_home, "spades.py"), "--truseq", "-t", "1", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), params]</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result = ["python3 " + os.path.join(spades_home, "spades.py"), "--truseq", "-t", "1", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), params]</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # result = ["./truspades.py", "-o", os.path.join(output_dir, barcode.id), reads_line(barcode.libs), " ".join(params), "\n"]</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> return " ".join(result)</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/projects/mts/scripts/bin_profiles.py</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/projects/mts/scripts/bin_profiles.py</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</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">@@ -212,6 +224,24 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="diff"> '''</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="diff"> A simple Python wrapper for the bh_tsne binary that makes it easier to use it</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -15,7 +15,7 @@</span> Example:</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> The output will not be normalised, maybe the below one-liner is of interest?:</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python -c 'import numpy; from sys import stdin, stdout;</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 -c 'import numpy; from sys import stdin, stdout;</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> d = numpy.loadtxt(stdin); d -= d.min(axis=0); d /= d.max(axis=0);</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> numpy.savetxt(stdout, d, fmt="%.8f", delimiter="\t")'</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -207,7 +207,7 @@</span> def run_bh_tsne(data, no_dims=2, perplex</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> os.waitpid(child_pid, 0)</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> except KeyboardInterrupt:</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Please run this program directly from python and not from ipython or jupyter.")</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Please run this program directly from python3 and not from ipython3 or jupyter.")</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> print("This is an issue due to asynchronous error handling.")</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> res = []</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/projects/mts/scripts/choose_bins.py</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/projects/mts/scripts/choose_bins.py</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="diff"><span class="p">@@ -1,5 +1,4 @@</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="354" 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="384" 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">@@ -354,3 +384,789 @@ Description: Make sure Python3 interpreter is used in scripts</td>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/corrector_logic.py</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/corrector_logic.py</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> </span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> ############################################################################</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> </span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> ############################################################################</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/compare_gaps_pos.py</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/compare_gaps_pos.py</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="p">@@ -1,5 +1,4 @@</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> </span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> ############################################################################</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/gap_finder.py</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/gap_finder.py</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/mis_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/mis_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/misassemblies.py</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies.py</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/run_viz.sh</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/run_viz.sh</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="p">@@ -13,9 +13,9 @@</span> touch list.txt</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> for file in $(ls *.stdout)</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> do</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python parser.py $file >> list.txt</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 parser.py $file >> list.txt</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python misassemblies.py -o plot -a list.txt --arcs</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 misassemblies.py -o plot -a list.txt --arcs</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> rm list.txt</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/reads_quality.py</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/reads_quality.py</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/cleancontigs/sort_contigs.py</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/cleancontigs/sort_contigs.py</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/analyze_sinks.py</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/analyze_sinks.py</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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487
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> ############################################################################</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/compare_fasta.py</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/compare_fasta.py</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> </span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> ############################################################################</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/compare_gaps.py</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/compare_gaps.py</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> </span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> ############################################################################</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/compare_runs.sh</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/compare_runs.sh</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="p">@@ -11,5 +11,5 @@</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> for file in $(ls $1/saves/*.sqn)</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> do</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> echo $(basename $file)</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file)</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file)</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> done</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/compare_used_snps.py</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/compare_used_snps.py</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> </span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> ############################################################################</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/parser.py</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/parser.py</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> </span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> ############################################################################</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/run_parser.sh</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/run_parser.sh</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="p">@@ -10,5 +10,5 @@</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> </span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> for file in $(ls *.stdout)</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> do</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python parser.py $file >> list.txt</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 parser.py $file >> list.txt</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/misc/sam_analyzer_2.py</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/misc/sam_analyzer_2.py</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> </span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="p">@@ -23,8 +23,8 @@</span> echo Building taxonomy index for $1 ...</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> echo Temporary file: $tempfile</span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> echo Index prefix: $indxfile</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python preprocessing.py < $1 > $tempfile</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 preprocessing.py < $1 > $tempfile</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> bowtie-build $tempfile $indxfile</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> </span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-rm $tempfile</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm $tempfile</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="p">@@ -24,4 +24,4 @@</span> fi</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> </span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> echo Analyzing taxonomy for $1 ...</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> </span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python parse_tax_from_bowtie.py</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python3 parse_tax_from_bowtie.py</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span> function clean_paired ()</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedleft > "${output_folder}/paired_log1_${timestamp}.tmp" 2> /dev/null</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedright > "${output_folder}/paired_log2_${timestamp}.tmp" 2> /dev/null</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> echo "running filter_reads.py"</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ${path_to_script}/../reads_utils/filter/filter_reads.py $cleanedleft $cleanedright "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ${path_to_script}/../reads_utils/filter/filter_reads.py $cleanedleft $cleanedright "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> mv $filteredleft $cleanedleft</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> mv $filteredright $cleanedright</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> done</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="p">@@ -199,7 +199,7 @@</span> do</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> then</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> echo "building index for sequence $i"</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> mkdir -p "${path_to_db}/index/${i:0:2}"</span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ${path_to_script}/read_fasta_using_index.py $i "${blast_database}.fasta" > "${i}.fasta.tmp"</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ${path_to_script}/read_fasta_using_index.py $i "${blast_database}.fasta" > "${i}.fasta.tmp"</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> bowtie-build "${i}.fasta.tmp" "${path_to_db}/index/${i:0:2}/${i}"</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> rm "${i}.fasta.tmp"</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> fi</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="p">@@ -220,7 +220,7 @@</span> then</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> else</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> ln -s $all_reads "${output_folder}/${filename}"</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> fi</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ${path_to_script}/../reads_utils/conversion/split_any_fastq.py "${output_folder}/${filename}"</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ${path_to_script}/../reads_utils/conversion/split_any_fastq.py "${output_folder}/${filename}"</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> filename=${filename%.*}</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> left="${output_folder}/${filename}_left.${extension}"</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> right="${output_folder}/${filename}_right.${extension}"</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/cleancontigs/cleancontigs.py</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/cleancontigs/cleancontigs.py</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> </span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> ############################################################################</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/get_misassembled_contigs.py</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/get_misassembled_contigs.py</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/texify_results.py</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/texify_results.py</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/contig_analysis/visualizer/main.py</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/contig_analysis/visualizer/main.py</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> </span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> ############################################################################</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/dataset_tar</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/dataset_tar</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="p">@@ -3,4 +3,4 @@</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> DIR="$( cd "$( dirname "$0" )" && pwd )"</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )"</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> pushd $BASE/data/input > /dev/null</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/loc_pic.py</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/loc_pic.py</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"> </span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"> ############################################################################</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/misc/gcc_version_check.py</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/misc/gcc_version_check.py</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> </span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/misc/sam_analysis_sorter.py</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/misc/sam_analysis_sorter.py</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/crop/crop_genome.py</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/crop/crop_genome.py</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/crop/paired_crop.py</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/crop/paired_crop.py</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/paired_reads_quality.py</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/paired_reads_quality.py</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/coverage.py</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/coverage.py</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/coverage_hist.py</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/coverage_hist.py</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/is.py</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/is.py</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/raw.py</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/raw.py</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/raws_w_orientation.py</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/raws_w_orientation.py</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/shift.py</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/shift.py</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/single_log_to_paired.py</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/single_log_to_paired.py</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> </span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> ############################################################################</span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/stat/trim.py</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/stat/trim.py</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python -O</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -O</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> </span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> ############################################################################</span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/spades_download_stats/filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/spades_download_stats/filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> #***************************************************************************</span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> ##* Copyright (c) 2011-2014 Saint-Petersburg Academic University</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="p">@@ -12,6 +12,6 @@</span> pushd ../../../</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> rm -rf spades_output/ECOLI_IS220_QUAKE_1K</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> ./spades.py --only-assembler --generate-sam-file -k 21,55 -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"> popd</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/estimation_deprecated/Nx_plot.py</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/estimation_deprecated/Nx_plot.py</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="p">@@ -1,3 +1,4 @@</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> ############################################################################</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> # Copyright (c) 2011-2014 Saint Petersburg Academic University</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="p">@@ -18,9 +19,9 @@</span> import fastaparser</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> if len(sys.argv) < 2:</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> print "Draws Nx plot (from N00 through N50 to N100)"</span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"> print</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Usage: python", sys.argv[0], "FASTA1 [FASTA2 [FASTA3 ..."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print "Usage: python3", sys.argv[0], "FASTA1 [FASTA2 [FASTA3 ..."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"> print</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Example: python", sys.argv[0], "../../data/debruijn/we_contigs.fasta ../../data/debruijn/velvet_contigs.fa"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print "Example: python3", sys.argv[0], "../../data/debruijn/we_contigs.fasta ../../data/debruijn/velvet_contigs.fa"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"> exit(0)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"> for filename in sys.argv[1:]:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/truseq/quast_all.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/truseq/quast_all.sh</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span> mkdir $3/tmp</span>
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<td class="diff-line-num new new_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> mkdir $3/all_reports</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"> ls $1 | xargs -P $4 -I {} -t quast --min-contig 1000 --contig-thresholds 5000,8000,12000 -e -R $2/{}.fasta $1/{}/scaffolds.fasta -o $3/tmp/{}</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"> ls $1 | xargs -P $4 -I {} -t cp $3/tmp/{}/report.tsv $3/all_reports/{}.tsv</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python quast_all.py $3/all_reports $3</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 quast_all.py $3/all_reports $3</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> grep "( inversion )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/inversions.txt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> grep "( translocation )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/translocations.txt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> grep "( relocation," $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/relocations.txt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="p">@@ -12,6 +12,6 @@</span> pushd ../../../</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"> rm -rf spades_output/ECOLI_IS220_QUAKE_1K</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"> ./spades.py -k 21,55 --only-assembler -1 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R /tmp/data/input/E.coli/MG1655-K12.fasta.gz -G /tmp/data/input/E.coli/genes/genes.gff -O /tmp/data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R /tmp/data/input/E.coli/MG1655-K12.fasta.gz -G /tmp/data/input/E.coli/genes/genes.gff -O /tmp/data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> popd</span>
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<td class="diff-line-num new new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/MR</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> </span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> rm -rf ~/quast-1.3/MRUBER_PRENORM/</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> </span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER_PRENORM/ /tmp/data/output/spades_output/MRUBER_PRENORM/contigs.fasta</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER_PRENORM/ /tmp/data/output/spades_output/MRUBER_PRENORM/contigs.fasta</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"> </span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/MRUBER_PRENORM/transposed_report.tsv 49100 16 2152 75.6 65 21</span></span>
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<td class="diff-line-num new new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/MRUBER_PRENORM/transposed_report.tsv 49100 16 2152 75.6 65 21</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> exitlvl=$?</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> popd</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"> </span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/projects/mts/binners/gattaca.snake</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/projects/mts/binners/gattaca.snake</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="p">@@ -32,8 +32,8 @@</span> rule gattaca:</span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"> threads: THREADS</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> log: "binning/gattaca.log"</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> message: "Running GATTACA clustering"</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- shell: "set +u; source activate py27; set -u\n"</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "python {SOFT}/gattaca/src/python/gattaca.py cluster --contigs {input.contigs}"</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shell: "set +u; source activate py37; set -u\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "python3 {SOFT}/gattaca/src/python/gattaca.py cluster --contigs {input.contigs}"</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"> " --coverage {input.profiles} --algorithm dirichlet --clusters {output} >{log} 2>&1\n"</span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"> "rm -f assembly/splits/all_filtered.fasta.fai"</span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"> </span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/EC</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> </span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_SC_LANE_1/</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> </span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1/contigs.fasta</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1/contigs.fasta</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> </span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1/transposed_report.tsv 108000 2 4080 96.4 4 0.7</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1/transposed_report.tsv 108000 2 4080 96.4 4 0.7</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> exitlvl=$?</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> popd</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/estimation_deprecated/README</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/estimation_deprecated/README</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> Prerequisites:</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> </span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sudo apt-get install python python-matplotlib python-numpy</span></span>
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<td class="diff-line-num new new_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sudo apt-get install python3 python3-matplotlib python3-numpy</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"><span class="p">@@ -11,6 +11,6 @@</span> set -e</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"> pushd ../../../</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"> rm -rf spades_output/ECOLI_1K_TEAMCITY_BH</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"> ./spades.py --only-error-correction -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_1K_TEAMCITY_BH</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/tools/reads_utils/reads_quality.py -r test_dataset/reference_1K.fa.gz -o spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results spades_output/ECOLI_1K_TEAMCITY_BH/corrected/dataset.info</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess_reads.py spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 100 100</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/tools/reads_utils/reads_quality.py -r test_dataset/reference_1K.fa.gz -o spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results spades_output/ECOLI_1K_TEAMCITY_BH/corrected/dataset.info</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess_reads.py spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 100 100</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"> popd</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/EC</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"> </span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1_BH_woHUMAN/contigs.fasta</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/ /tmp/data/output/spades_output/ECOLI_SC_LANE_1_BH_woHUMAN/contigs.fasta</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"> </span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/transposed_report.tsv 85000 7</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/transposed_report.tsv 85000 7</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"> exitlvl=$?</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> popd</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"> </span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/MR</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"> </span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"> rm -rf ~/quast-1.3/MRUBER/</span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"> </span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER/ /tmp/data/output/spades_output/MRUBER/contigs.fasta</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/M.ruber/ref.fasta -G data/input/M.ruber/MRU_genes.txt -o ~/quast-1.3/MRUBER/ /tmp/data/output/spades_output/MRUBER/contigs.fasta</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/MRUBER/transposed_report.tsv 20000 20 1500 50.0 30 10</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/MRUBER/transposed_report.tsv 20000 20 1500 50.0 30 10</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> exitlvl=$?</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"> popd</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> </span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/PM</span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"> </span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"> rm -rf ~/quast-1.3/PMARINUS/</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/P.marinus/ref.fasta -o ~/quast-1.3/PMARINUS/ /tmp/data/output/spades_output/PMARINUS/contigs.fasta</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/P.marinus/ref.fasta -o ~/quast-1.3/PMARINUS/ /tmp/data/output/spades_output/PMARINUS/contigs.fasta</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"> </span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/PMARINUS/transposed_report.tsv 292000 0 1612 95.3 3.4 1.5</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/PMARINUS/transposed_report.tsv 292000 0 1612 95.3 3.4 1.5</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"> exitlvl=$?</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"> popd</span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"> </span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/SA</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"> </span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"> rm -rf ~/quast-1.3/SAUREUS_LANE_7/</span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/S.aureus/USA300_FPR3757.fasta -G data/input/S.aureus/genes/bacteria_genes.txt -o ~/quast-1.3/SAUREUS_LANE_7/ /tmp/data/output/spades_output/SAUREUS_LANE_7/contigs.fasta</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/S.aureus/USA300_FPR3757.fasta -G data/input/S.aureus/genes/bacteria_genes.txt -o ~/quast-1.3/SAUREUS_LANE_7/ /tmp/data/output/spades_output/SAUREUS_LANE_7/contigs.fasta</span></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"> </span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/SAUREUS_LANE_7/transposed_report.tsv 85000 7 2500 99.8 6 6</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/SAUREUS_LANE_7/transposed_report.tsv 85000 7 2500 99.8 6 6</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"> exitlvl=$?</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"> popd</span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"> </span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="p">@@ -1,4 +1,3 @@</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"> #!/bin/bash</span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"> </span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"> ############################################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"><span class="p">@@ -13,6 +12,6 @@</span> pushd ../../../</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"> rm -rf /tmp/data/output/spades_output/ECOLI_IS480_QUAKE</span>
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<td class="diff-line-num new new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"> ./spades.py --only-assembler -k 21,33,55 -m 12 -1 data/input/E.coli/is480/ERR022075_1.cor.fastq.gz -2 data/input/E.coli/is480/ERR022075_2.cor.fastq.gz -s data/input/E.coli/is480/ERR022075_1.cor_single.fastq.gz -s data/input/E.coli/is480/ERR022075_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS480_QUAKE</span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_IS480_QUAKE/</span>
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<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS480_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS480_QUAKE/contigs.fasta</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS480_QUAKE/transposed_report.tsv 133000 4</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS480_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS480_QUAKE/contigs.fasta</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS480_QUAKE/transposed_report.tsv 133000 4</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="diff"> popd</span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/EC</span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="diff"> </span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7_PRENORM/contigs.fasta</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7_PRENORM/contigs.fasta</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="diff"> </span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/transposed_report.tsv 115000 4 4240 99.8 4 0.8</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/transposed_report.tsv 115000 4 4240 99.8 4 0.8</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="diff"> exitlvl=$?</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="diff"> popd</span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="diff"> </span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/teamcity.py</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/teamcity.py</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"> </span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"> ############################################################################</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="diff"> # Copyright (c) 2015-2017 Saint Petersburg State University</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span> from teamcity_support import *</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="diff"> ### main ###</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="diff"> try:</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="diff"> if len(sys.argv) == 1:</span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = 'python {} -h'.format(sys.argv[0])</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = 'python3 {} -h'.format(sys.argv[0])</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="diff"> subprocess.call(command, shell=True)</span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="diff"> sys.exit(1)</span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="diff"> </span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="diff"><span class="p">@@ -1,4 +1,3 @@</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="diff"> #!/bin/bash</span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="diff"> </span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="diff"> ############################################################################</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="diff"><span class="p">@@ -13,6 +12,6 @@</span> pushd ../../../</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="diff"> rm -rf /tmp/data/output/spades_output/ECOLI_IS220_QUAKE</span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="diff"> ./spades.py --generate-sam-file --only-assembler -m 12 -k 21,33,55 -1 data/input/E.coli/is220/s_6_1.cor.fastq.gz -2 data/input/E.coli/is220/s_6_2.cor.fastq.gz -s data/input/E.coli/is220/s_6_1.cor_single.fastq.gz -s data/input/E.coli/is220/s_6_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS220_QUAKE</span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE/</span>
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<td class="diff-line-num new new_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS220_QUAKE/contigs.fasta</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE/transposed_report.tsv 80000 3</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS220_QUAKE/contigs.fasta</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE/transposed_report.tsv 80000 3</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="diff"> popd</span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/EC</span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="diff"> rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7/</span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7/contigs.fasta</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_SC_JGI_LANE_7/ /tmp/data/output/spades_output/ECOLI_SC_JGI_LANE_7/contigs.fasta</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="diff"> </span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7/transposed_report.tsv 115000 4 4260 99.8 3.2 0.7</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_SC_JGI_LANE_7/transposed_report.tsv 115000 4 4260 99.8 3.2 0.7</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="diff"> exitlvl=$?</span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="diff"> popd</span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="diff"> </span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="diff"><span class="p">@@ -17,9 +17,9 @@</span> rm -rf /tmp/data/output/spades_output/PH</span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="diff"> </span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="diff"> rm -rf ~/quast-1.3/PHEPARINUS_PRENORM/</span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="diff"> </span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS_PRENORM/ /tmp/data/output/spades_output/PHEPARINUS_PRENORM/contigs.fasta</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS_PRENORM/ /tmp/data/output/spades_output/PHEPARINUS_PRENORM/contigs.fasta</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="diff"> </span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS_PRENORM/transposed_report.tsv 160000 9 3900 95.5 10.0 1.0</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS_PRENORM/transposed_report.tsv 160000 9 3900 95.5 10.0 1.0</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="diff"> exitlvl=$?</span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="diff"> popd</span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/estimation/run_real.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/estimation/run_real.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="diff"><span class="p">@@ -1,3 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/bin/sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="diff"> ############################################################################</span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="diff"> # Copyright (c) 2011-2014 Saint Petersburg Academic University</span>
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<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="diff"><span class="p">@@ -5,4 +6,4 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="diff"> # See file LICENSE for details.</span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"> ############################################################################</span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/res_counter/run.pl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/res_counter/run.pl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span> print "started...\n";</span>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"> my $stat_proc = fork;</span>
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<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"> if ($stat_proc == 0) {</span>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exec "python $script_dir/stats_counter.py $child 1>>rc_stats.txt 2>>rc_stats.txt";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exec "python3 $script_dir/stats_counter.py $child 1>>rc_stats.txt 2>>rc_stats.txt";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="diff"> </span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="diff"> waitpid($child, 0);</span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="diff"><span class="p">@@ -11,6 +11,6 @@</span> set -e</span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"> pushd ../../../</span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="diff"> rm -rf /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH</span>
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<td class="diff-line-num new new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="diff"> ./spades.py --sc --only-error-correction --12 ./data/input/E.coli/sc_lane_1/ecoli_mda_lane1.fastq.gz -m 160 -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH</span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/tools/reads_utils/reads_quality.py -r data/input/E.coli/MG1655-K12.fasta.gz -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/corrected/dataset.info</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess_reads.py /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 90 97 # 97 97</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/tools/reads_utils/reads_quality.py -r data/input/E.coli/MG1655-K12.fasta.gz -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/corrected/dataset.info</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess_reads.py /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 90 97 # 97 97</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="diff"> popd</span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/update_threshold.py</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/update_threshold.py</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"> ############################################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"> # Copyright (c) 2015 Saint Petersburg State University</span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"><span class="p">@@ -264,7 +264,7 @@</span> def check_args(args):</span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="diff"> ### main ###</span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="diff"> try:</span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="diff"> if len(sys.argv) == 1:</span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = 'python {} -h'.format(sys.argv[0])</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = 'python3 {} -h'.format(sys.argv[0])</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="diff"> subprocess.call(command, shell=True)</span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="diff"> sys.exit(1)</span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="diff"> </span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/full_run.sh</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/full_run.sh</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="diff"><span class="p">@@ -1,10 +1,3 @@</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="diff"> #!/bin/bash</span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="diff"> </span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="diff"> ############################################################################</span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="diff"><span class="p">@@ -26,7 +19,7 @@</span> mkdir $project_dir -p</span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="diff"> read line < $options_dir"spades.options"</span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="diff"> echo $line</span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="diff"> ./cpcfg</span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python2.6 ./spades.py $line -o $project_dir --disable-gzip-output --mismatch-correction</span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ./spades.py $line -o $project_dir --disable-gzip-output --mismatch-correction</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="diff"> read line < $options_dir"quast.options"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="diff"> echo $line</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="diff"><span class="p">@@ -45,7 +38,7 @@</span> cp $work_contigs $dir$(date +%Y%m%d_%H%M</span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="diff"> cp $project_dir"/scaffolds.fasta" $dir$(date +%Y%m%d_%H%M%S)_scaf".fasta"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python2.6 ~/quast-1.3/quast.py $work_contigs $line -o $project_dir"/quality_results/"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py $work_contigs $line -o $project_dir"/quality_results/"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="diff"> rm $dir"/quast_all" -rf</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="diff"> #echo $dir"*.fasta" $line -o $dir"/quast_all"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="diff"> dirtmp=$dir"tmp/"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="diff"><span class="p">@@ -60,7 +53,7 @@</span> for i in $dir*.fasta ; do</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="diff"> # echo $j</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="diff"> if [ -f $j ] ;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="diff"> then</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- compare_res=$(python2.6 ~/algorithmic-biology/assembler/src/tools/contig_analysis/compare_fasta.py $i $j)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compare_res=$(python3 ~/algorithmic-biology/assembler/src/tools/contig_analysis/compare_fasta.py $i $j)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="diff"> # echo $compare_res</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="diff"> if [ $compare_res = "True" ]; </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="diff"> then</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="diff"><span class="p">@@ -79,8 +72,8 @@</span> quast_line="$output_pref/quast-1.3/quast</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="diff"> quast1_2_line="$output_pref/quast-1.2/quast.py -M 500 $dirtmp* $line -o $dir/quast1_2_all/"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="diff"> echo "$quast_line"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python2.6 $quast_line >null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python2.6 $quast1_2_line >null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 $quast_line >null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 $quast1_2_line >null</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="diff"> ssh -n antipov@194.85.238.21 mkdir -p "/var/www/teamcity_runs/$1$2" &</span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="diff"><span class="p">@@ -98,7 +91,7 @@</span> do</span>
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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="diff"> splitted_opts=$splitted_opts" "${opts[$i * 2 + 1]}</span>
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<td class="diff-line-num new new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="diff"> done</span>
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<td class="diff-line-num new new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="diff"> echo $splitted_opts</span>
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<td class="diff-line-num new old_line" data-linenumber="357" style="width: 35px; color: rgba(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="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py $project_dir"quality_results/transposed_report.tsv" $splitted_opts</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py $project_dir"quality_results/transposed_report.tsv" $splitted_opts</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="diff"> rm $project_dir"/corrected/" -rf</span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="diff"><span class="p">@@ -12,6 +12,6 @@</span> pushd ../../../</span>
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<td class="diff-line-num new new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="diff"> rm -rf /tmp/data/output/spades_output/BFAECIUM_QUAKE</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="diff"> ./spades.py -k 21,33,55 -m 16 --only-assembler -1 data/input/B.faecium/std_left.cor.fastq.gz -2 data/input/B.faecium/std_right.cor.fastq.gz -s data/input/B.faecium/std_right.cor_single.fastq.gz -s data/input/B.faecium/std_left.cor_single.fastq.gz -o /tmp/data/output/spades_output/BFAECIUM_QUAKE</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="diff"> rm -rf ~/quast-1.3/BFAECIUM_QUAKE/</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R /tmp/data/input/B.faecium/ref.fasta.gz -o ~/quast-1.3/BFAECIUM_QUAKE/ /tmp/data/output/spades_output/BFAECIUM_QUAKE/contigs.fasta</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/BFAECIUM_QUAKE/transposed_report.tsv 330000 0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R /tmp/data/input/B.faecium/ref.fasta.gz -o ~/quast-1.3/BFAECIUM_QUAKE/ /tmp/data/output/spades_output/BFAECIUM_QUAKE/contigs.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/BFAECIUM_QUAKE/transposed_report.tsv 330000 0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="diff"> popd</span>
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<td class="diff-line-num new new_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="diff"><span class="p">@@ -17,8 +17,8 @@</span> rm -rf /tmp/data/output/spades_output/PH</span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="diff"> </span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="diff"> rm -rf ~/quast-1.3/PHEPARINUS/</span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS/ /tmp/data/output/spades_output/PHEPARINUS/contigs.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS/transposed_report.tsv 140000 6 4140 98.0 8.0 2.0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 ~/quast-1.3/quast.py -R data/input/P.heparinus/ref.fasta -G data/input/P.heparinus/PHE_genes.txt -o ~/quast-1.3/PHEPARINUS/ /tmp/data/output/spades_output/PHEPARINUS/contigs.fasta</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 src/test/teamcity/assess.py ~/quast-1.3/PHEPARINUS/transposed_report.tsv 140000 6 4140 98.0 8.0 2.0</span></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="diff"> exitlvl=$?</span>
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<td class="diff-line-num new new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="diff"> popd</span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="diff"> </span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/spades_dev.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/spades_dev.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="diff"><span class="p">@@ -8,5 +8,5 @@</span> mkdir -p bin;</span>
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<td class="diff-line-num new new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="diff"> rm bin/*;</span>
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<td class="diff-line-num new new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="diff"> cp build/release/debruijn/spades bin/spades;</span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="diff"> cp build/release/hammer/hammer bin/hammer;</span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python spades.py "$@";</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 spades.py "$@";</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="diff"> </span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/dataset_hammer</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/dataset_hammer</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="diff"> DIR="$( cd "$( dirname "$0" )" && pwd )"</span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="diff"> BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )"</span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="diff"> #pushd $BASE/data/input > /dev/null</span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python $BASE/src/tools/dataset.py hammer $1</span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 $BASE/src/tools/dataset.py hammer $1</span></span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="diff"> #src/tools/dataset_hammer /mnt/ace/acestorage/snikolenko/090408_ultrashort/09</span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="diff"> #src/tools/dataset_hammer /mnt/ace/acestorage/data/input/x5/makarich.fbb.msu.ru/run1_fca/Quaked/</span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="diff"> #src/tools/dataset_hammer ~/temp/02</span></pre>
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<li id="6b4e31cdf8f9338db47a4fa236a08014b3851935">
<a href="https://salsa.debian.org/med-team/spades/commit/2dd0d58b8f01d2914d2d134c21123ade6d05f28b#6b4e31cdf8f9338db47a4fa236a08014b3851935"><strong>debian/patches/yaml_load.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,42 @@ Description: Specify yaml loader</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> support.pretty_print_reads(dataset_data, log)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -425,7 +425,7 @@</span> def fill_cfg(options_to_parse, log, seco</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> if load_processed_dataset:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> if os.path.isfile(processed_dataset_fpath):</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> except pyyaml.YAMLError:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> existing_dataset_data = None</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if existing_dataset_data is not None:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -433,7 +433,7 @@</span> def fill_cfg(options_to_parse, log, seco</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> else:</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if options_storage.dataset_yaml_filename:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> try:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'))</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> except pyyaml.YAMLError:</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> _, exc, _ = sys.exc_info()</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> support.error('exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -792,7 +792,7 @@</span> def main(args):</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> and not options_storage.restart_from == "ec":</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> if not bh_cfg.gzip_output or \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))):</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r')), Loader=pyyaml.FullLoader):</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> ec_is_needed = False</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> else:</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -869,7 +869,7 @@</span> def main(args):</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> support.continue_from_here(log)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> if os.path.isfile(corrected_dataset_yaml_filename):</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> if spades_cfg.disable_rr:</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> spades_cfg.__dict__["rr_enable"] = False</span>
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17
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/hammer_logic.py</span></span>
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18
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/hammer_logic.py</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span> def prepare_config_ih(filename, cfg, ext</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">@@ -34,3 +70,36 @@ Description: Specify yaml loader</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> remove_not_corrected_reads(cfg.output_dir)</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> is_changed = False</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> if cfg.gzip_output:</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/spades_logic.py</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/spades_logic.py</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span> def get_read_length(output_dir, K, ext_p</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> import pyyaml2 as pyyaml</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> elif sys.version.startswith('3.'):</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> import pyyaml3 as pyyaml</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- est_params_data = pyyaml.load(open(est_params_filename, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ est_params_data = pyyaml.load(open(est_params_filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> max_read_length = int(est_params_data['nomerge max read length'])</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> log.info("Max read length detected as %d" % max_read_length)</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> if max_read_length == 0:</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/spades_pipeline/corrector_logic.py</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/spades_pipeline/corrector_logic.py</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span> def prepare_config_corr(filename, cfg, e</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> import pyyaml2 as pyyaml</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> elif sys.version.startswith('3.'):</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> import pyyaml3 as pyyaml</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- data = pyyaml.load(open(filename, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> data["dataset"] = cfg.dataset</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> data["output_dir"] = cfg.output_dir</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> data["work_dir"] = cfg.tmp_dir</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/assembler/src/tools/reads_utils/reads_quality.py</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/assembler/src/tools/reads_utils/reads_quality.py</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -148,7 +148,7 @@</span> print("Analyzing datasets")</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> for dataset in datasets:</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dataset_data = pyyaml.load(file(dataset, 'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dataset_data = pyyaml.load(file(dataset, 'r'), Loader=pyyaml.FullLoader)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> except pyyaml.YAMLError, exc:</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> support.warning('skipping ' + dataset + ': exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> continue</span></pre>
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