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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gff2aplot">Debian Med / gff2aplot</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/c06763b8734ef0fa3527b8d2e3c5e08b6b48150a">c06763b8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T14:51:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure scripts will be found
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/7eaea1fe1e0becc8047ceae2e8ec764507e388b9">7eaea1fe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T14:58:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Suppress another error and avoid a warning
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1059c3645d4481142e798e809fdde14d8eed783a">
debian/patches/perl_5.28.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1059c3645d4481142e798e809fdde14d8eed783a">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/be4070ad1aa3bcce0881a0a074183d8be5db6019...7eaea1fe1e0becc8047ceae2e8ec764507e388b9#1059c3645d4481142e798e809fdde14d8eed783a"><strong>debian/patches/perl_5.28.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,7 +4,7 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/gff2aplot.pl</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/gff2aplot.pl</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1733,7 +173<span class="idiff left right">3</span>,7 @@ sub varscheck() {</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1733,7 +173<span class="idiff left right">4</span>,7 @@ sub varscheck() {</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> || return $F;</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> $flag && do {</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> my @tmpary = ();</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -13,3 +13,26 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> @{ $varec->{$class}{ $$rec[1] } } = ();</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> };</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> @tmpary = &find_regexp( $$rec[0] );</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2930,7 +2931,8 @@ sub set_page_axes() {</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> $vrf->{alignment_name}, 2;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elsif ( scalar( @{ $Order{ALN} } ) > 0 ) {</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elsif ( $Order{ALN} &&</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;">+ scalar( @{ $Order{ALN} } ) > 0 ) {</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> $Order{ALN}[0][0], 2;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3730,7 +3732,11 @@ sub fill_mid() {</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> sub counter { # $_[0]~current_pos++ $_[1]~char</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> my $str;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $str = "$_[1]";</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( length scalar(@_) == 1 ) {</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $str = "";</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else {</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $str = "$_[1]";</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> ( ( $_[0] % 50 ) == 0 )</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> && ( $str .= " [" . &fill_left( $_[0], 6, "0" ) . "]\n" );</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> &prt_to_stderr($str);</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/be4070ad1aa3bcce0881a0a074183d8be5db6019...7eaea1fe1e0becc8047ceae2e8ec764507e388b9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ ERR=0</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>script <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> README<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: teal;">$script</span><span class="k" style="font-weight: 600;">)</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Suppress verbose output for testing</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'/^[[:space:]]\+--verbose[[:space:]]\+\\$/d'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/--verbose//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/MG *-verbose/MG -quiet/'</span> README</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'/^[[:space:]]\+--verbose[[:space:]]\+\\$/d'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/--verbose//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/MG *-verbose/MG -quiet/'</span> <span class="nt" style="color: navy;"><span class="idiff left">-e</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'s?$BIN/\([a-z0-9]\+\).pl?\1?'</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'s?^$BIN/??'</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'1i set -x'</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-e</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'1i set -e'</span></span><span class="idiff right"> </span>README</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> sh README | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^KCRB.GT.hs-mm.log'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^|'</span> <span class="k" style="font-weight: 600;">*</span>.log <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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25
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ERR</span><span class="o" style="font-weight: 600;">=</span>1</span>
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