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From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
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Subject: [Seqan-dev] Reading fastq records - missing records?
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Hi Team,

here is another question:
Following code reads a fastq-file.
The file I'm testing on has 263333413 records:

> $ zcat C563WACXX_1.fastq.gz | wc -l
> 1053333652


The problem is, that the code seems to only read
the first 4000000 records. I don't understand why.

Can you advise me here?

Thank you,
Alexander

PS: I removed try/catch for better readability

seqan::StringSet<seqan::CharString> ids;
> seqan::StringSet<seqan::Dna5QString> seqs;
> seqan::StringSet<seqan::CharString> quals;
> unsigned batchSize = 10000;
> do {
> seqan::clear(ids); seqan::clear(seqs); seqan::clear(quals);
> readRecords(ids, seqs, quals, inputFile, batchSize);
> processRecords(ids, seqs, quals, barcodeGraph, vertexFilePtrMap);
> totalProcessed += seqan::length(ids);
> std::cout << "\r";
> std::cout << "reads processed in total: " << totalProcessed;
> std::cout.flush();
> } while(seqan::length(ids) > 0);

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<div dir=3D"ltr">Hi Team,<div><br></div><div>here is another question:</div=
><div>Following code reads a fastq-file.</div><div>The file I&#39;m testing=
 on has=C2=A0263333413 records:</div><div><blockquote class=3D"gmail_quote"=
 style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:=
rgb(204,204,204);border-left-style:solid;padding-left:1ex">$ zcat C563WACXX=
_1.fastq.gz | wc -l<br>1053333652</blockquote></div><div><br></div><div>The=
 problem is, that the code seems to only read</div><div>the first=C2=A04000=
000 records. I don&#39;t understand why.</div><div><br></div><div>Can you a=
dvise me here?</div><div><br></div><div>Thank you,</div><div>Alexander</div=
><div><br></div><div>PS: I removed try/catch for better readability</div><d=
iv><br><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;=
border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:=
solid;padding-left:1ex">seqan::StringSet&lt;seqan::CharString&gt; ids;<br>s=
eqan::StringSet&lt;seqan::Dna5QString&gt; seqs;<br>seqan::StringSet&lt;seqa=
n::CharString&gt; quals;<br>unsigned batchSize =3D 10000;<br>do {<br>seqan:=
:clear(ids);=C2=A0seqan::clear(seqs);=C2=A0seqan::clear(quals);<br>readReco=
rds(ids, seqs, quals, inputFile, batchSize);<br>processRecords(ids, seqs, q=
uals, barcodeGraph, vertexFilePtrMap);<br>totalProcessed +=3D seqan::length=
(ids);<br>std::cout &lt;&lt; &quot;\r&quot;;<br>std::cout &lt;&lt; &quot;re=
ads processed in total: &quot; &lt;&lt; totalProcessed;<br>std::cout.flush(=
);<br>} while(seqan::length(ids) &gt; 0);</blockquote></div></div>

--089e013cbeac30d7680517771e14--



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From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
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Subject: [Seqan-dev] Infix of const String
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Hi Team,

adopting from IndexIterators Tutorial, following problem came up:

When I want to save an Infix of an representative in an Index Iterator:

seqan::Infix<TBarcodeString>::Type referenceIfx =3D
> infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);


the error pops up, that I can't use a const String for this:

/opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42: error:
> invalid conversion from =E2=80=98seqan::Pointer_<const
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<> > >::Type {aka const
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<> >*}=E2=80=99 to
> =E2=80=98seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char,
> seqan::Dna5_>, seqan::Alloc<> > >::Type {aka
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<> >*}=E2=80=99 [-fpermissive]
>          data_host(_toPointer(host(_other))),


Solutions?

Best,
Alexander

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<div dir=3D"ltr">Hi Team,<div><br></div><div>adopting from IndexIterators T=
utorial, following problem came up:</div><div><br></div><div>When I want to=
 save an Infix of an representative in an Index Iterator:</div><div><br></d=
iv><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;bord=
er-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:soli=
d;padding-left:1ex">seqan::Infix&lt;TBarcodeString&gt;::Type referenceIfx =
=3D infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);</=
blockquote><div><br></div><div>the error pops up, that I can&#39;t use a co=
nst String for this:</div><div><br></div><div><blockquote class=3D"gmail_qu=
ote" style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-co=
lor:rgb(204,204,204);border-left-style:solid;padding-left:1ex">/opt/seqan/s=
eqan-src/include/seqan/sequence/segment_infix.h:135:42: error: invalid conv=
ersion from =E2=80=98seqan::Pointer_&lt;const seqan::String&lt;seqan::Simpl=
eType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt; &gt;::T=
ype {aka const seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan::=
Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=80=99 to =E2=80=98seqan::Pointer_=
&lt;seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, =
seqan::Alloc&lt;&gt; &gt; &gt;::Type {aka seqan::String&lt;seqan::SimpleTyp=
e&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=80=99 =
[-fpermissive]<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0data_host(_toPointer(ho=
st(_other))),</blockquote><div><br></div><div>Solutions?</div><div><br></di=
v><div>Best,</div><div>Alexander=C2=A0</div></div></div>

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Subject: Re: [Seqan-dev] Reading fastq records - missing records?
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i dont know why, but maybe because your memory doesn't enough?

2015-06-01 23:14 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.com>
:

> Hi Team,
>
> here is another question:
> Following code reads a fastq-file.
> The file I'm testing on has 263333413 records:
>
>> $ zcat C563WACXX_1.fastq.gz | wc -l
>> 1053333652
>
>
> The problem is, that the code seems to only read
> the first 4000000 records. I don't understand why.
>
> Can you advise me here?
>
> Thank you,
> Alexander
>
> PS: I removed try/catch for better readability
>
> seqan::StringSet<seqan::CharString> ids;
>> seqan::StringSet<seqan::Dna5QString> seqs;
>> seqan::StringSet<seqan::CharString> quals;
>> unsigned batchSize = 10000;
>> do {
>> seqan::clear(ids); seqan::clear(seqs); seqan::clear(quals);
>> readRecords(ids, seqs, quals, inputFile, batchSize);
>> processRecords(ids, seqs, quals, barcodeGraph, vertexFilePtrMap);
>> totalProcessed += seqan::length(ids);
>> std::cout << "\r";
>> std::cout << "reads processed in total: " << totalProcessed;
>> std::cout.flush();
>> } while(seqan::length(ids) > 0);
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

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<div dir=3D"ltr">i dont know why, but maybe because your memory doesn&#39;t=
 enough?</div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">201=
5-06-01 23:14 GMT+07:00 Alexander Vowinkel <span dir=3D"ltr">&lt;<a href=3D=
"mailto:vowinkel.alexander@gmail.com" target=3D"_blank">vowinkel.alexander@=
gmail.com</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" style=3D"mar=
gin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr=
">Hi Team,<div><br></div><div>here is another question:</div><div>Following=
 code reads a fastq-file.</div><div>The file I&#39;m testing on has=C2=A026=
3333413 records:</div><div><blockquote class=3D"gmail_quote" style=3D"margi=
n:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204=
);border-left-style:solid;padding-left:1ex">$ zcat C563WACXX_1.fastq.gz | w=
c -l<br>1053333652</blockquote></div><div><br></div><div>The problem is, th=
at the code seems to only read</div><div>the first=C2=A04000000 records. I =
don&#39;t understand why.</div><div><br></div><div>Can you advise me here?<=
/div><div><br></div><div>Thank you,</div><div>Alexander</div><div><br></div=
><div>PS: I removed try/catch for better readability</div><div><br><blockqu=
ote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left-wid=
th:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-l=
eft:1ex">seqan::StringSet&lt;seqan::CharString&gt; ids;<br>seqan::StringSet=
&lt;seqan::Dna5QString&gt; seqs;<br>seqan::StringSet&lt;seqan::CharString&g=
t; quals;<br>unsigned batchSize =3D 10000;<br>do {<br>seqan::clear(ids);=C2=
=A0seqan::clear(seqs);=C2=A0seqan::clear(quals);<br>readRecords(ids, seqs, =
quals, inputFile, batchSize);<br>processRecords(ids, seqs, quals, barcodeGr=
aph, vertexFilePtrMap);<br>totalProcessed +=3D seqan::length(ids);<br>std::=
cout &lt;&lt; &quot;\r&quot;;<br>std::cout &lt;&lt; &quot;reads processed i=
n total: &quot; &lt;&lt; totalProcessed;<br>std::cout.flush();<br>} while(s=
eqan::length(ids) &gt; 0);</blockquote></div></div>
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seqan-dev mailing list<br>
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i don't know, but when i using my program it's work perfectly, of course i
using another type (not TBarcodeString).

here my example:

DnaString mySekuens  =3D "ACGTACGTACGT";

startPosition =3D 0;
endPosition =3D startPosition + 5;

Infix<String<Dna> >::Type inf;
inf =3D infix(mySekuens, startPosition, endPosition);


the output  ACGTA;

2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.com>=
:

> Hi Team,
>
> adopting from IndexIterators Tutorial, following problem came up:
>
> When I want to save an Infix of an representative in an Index Iterator:
>
> seqan::Infix<TBarcodeString>::Type referenceIfx =3D
>> infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);
>
>
> the error pops up, that I can't use a const String for this:
>
> /opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42: error=
:
>> invalid conversion from =E2=80=98seqan::Pointer_<const
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> > >::Type {aka const
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> >*}=E2=80=99 to
>> =E2=80=98seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char,
>> seqan::Dna5_>, seqan::Alloc<> > >::Type {aka
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> >*}=E2=80=99 [-fpermissive]
>>          data_host(_toPointer(host(_other))),
>
>
> Solutions?
>
> Best,
> Alexander
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

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<div dir=3D"ltr">i don&#39;t know, but when i using my program it&#39;s wor=
k perfectly, of course i using another type (not=C2=A0<span style=3D"font-s=
ize:13px">TBarcodeString).</span><div><span style=3D"font-size:13px"><br></=
span></div><div><span style=3D"font-size:13px">here my example:</span></div=
><div><span style=3D"font-size:13px"><br></span></div><div><span style=3D"f=
ont-size:13px">DnaString mySekuens =C2=A0=3D &quot;ACGTACGTACGT&quot;;</spa=
n></div><div><span style=3D"font-size:13px"><br></span></div><div><span sty=
le=3D"font-size:13px">startPosition =3D 0;</span></div><div><span style=3D"=
font-size:13px">endPosition =3D startPosition + 5;</span></div><div><span s=
tyle=3D"font-size:13px"><br></span></div><div>Infix&lt;String&lt;Dna&gt; &g=
t;::Type inf;<br></div><div>inf =3D infix(mySekuens, startPosition, endPosi=
tion);</div><div><br></div><div><br></div><div>the output =C2=A0<span style=
=3D"font-size:13px">ACGTA;</span></div></div><div class=3D"gmail_extra"><br=
><div class=3D"gmail_quote">2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <s=
pan dir=3D"ltr">&lt;<a href=3D"mailto:vowinkel.alexander@gmail.com" target=
=3D"_blank">vowinkel.alexander@gmail.com</a>&gt;</span>:<br><blockquote cla=
ss=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;pa=
dding-left:1ex"><div dir=3D"ltr">Hi Team,<div><br></div><div>adopting from =
IndexIterators Tutorial, following problem came up:</div><div><br></div><di=
v>When I want to save an Infix of an representative in an Index Iterator:</=
div><div><br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0p=
x 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border=
-left-style:solid;padding-left:1ex">seqan::Infix&lt;TBarcodeString&gt;::Typ=
e referenceIfx =3D infix(representative(indexIt), parentRepLength(indexIt) =
+ 1, endPos);</blockquote><div><br></div><div>the error pops up, that I can=
&#39;t use a const String for this:</div><div><br></div><div><blockquote cl=
ass=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px=
;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1e=
x">/opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42: erro=
r: invalid conversion from =E2=80=98seqan::Pointer_&lt;const seqan::String&=
lt;seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&g=
t; &gt; &gt;::Type {aka const seqan::String&lt;seqan::SimpleType&lt;unsigne=
d char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=80=99 to =E2=80=98=
seqan::Pointer_&lt;seqan::String&lt;seqan::SimpleType&lt;unsigned char, seq=
an::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt; &gt;::Type {aka seqan::String&lt;s=
eqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &=
gt;*}=E2=80=99 [-fpermissive]<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0data_hos=
t(_toPointer(host(_other))),</blockquote><div><br></div><div>Solutions?</di=
v><div><br></div><div>Best,</div><div>Alexander=C2=A0</div></div></div>
<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de">seqan-dev@lists.fu-berlin.d=
e</a><br>
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>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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Hi Fadhlan,

why should memory be an issue?
I can load 400 of 10000 sized batches.
I always clear the Sets that save the sequences
after they were used.

Best,
Alexander

2015-06-02 23:36 GMT-05:00 Fadhlan Rizal <fadhlan.fari@gmail.com>:

> i dont know why, but maybe because your memory doesn't enough?
>
> 2015-06-01 23:14 GMT+07:00 Alexander Vowinkel <
> vowinkel.alexander@gmail.com>:
>
>> Hi Team,
>>
>> here is another question:
>> Following code reads a fastq-file.
>> The file I'm testing on has 263333413 records:
>>
>>> $ zcat C563WACXX_1.fastq.gz | wc -l
>>> 1053333652
>>
>>
>> The problem is, that the code seems to only read
>> the first 4000000 records. I don't understand why.
>>
>> Can you advise me here?
>>
>> Thank you,
>> Alexander
>>
>> PS: I removed try/catch for better readability
>>
>> seqan::StringSet<seqan::CharString> ids;
>>> seqan::StringSet<seqan::Dna5QString> seqs;
>>> seqan::StringSet<seqan::CharString> quals;
>>> unsigned batchSize = 10000;
>>> do {
>>> seqan::clear(ids); seqan::clear(seqs); seqan::clear(quals);
>>> readRecords(ids, seqs, quals, inputFile, batchSize);
>>> processRecords(ids, seqs, quals, barcodeGraph, vertexFilePtrMap);
>>> totalProcessed += seqan::length(ids);
>>> std::cout << "\r";
>>> std::cout << "reads processed in total: " << totalProcessed;
>>> std::cout.flush();
>>> } while(seqan::length(ids) > 0);
>>
>>
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>
>>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

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<div dir=3D"ltr">Hi Fadhlan,<div><br></div><div>why should memory be an iss=
ue?</div><div>I can load 400 of=C2=A0<span style=3D"font-size:12.8000001907=
349px">10000 sized batches.</span></div><div><span style=3D"font-size:12.80=
00001907349px">I always clear the Sets that save the sequences</span></div>=
<div><span style=3D"font-size:12.8000001907349px">after they were used.</sp=
an></div><div><br></div><div><span style=3D"font-size:12.8000001907349px">B=
est,</span></div><div><span style=3D"font-size:12.8000001907349px">Alexande=
r</span></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quot=
e">2015-06-02 23:36 GMT-05:00 Fadhlan Rizal <span dir=3D"ltr">&lt;<a href=
=3D"mailto:fadhlan.fari@gmail.com" target=3D"_blank">fadhlan.fari@gmail.com=
</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0=
 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr">i dont =
know why, but maybe because your memory doesn&#39;t enough?</div><div class=
=3D"gmail_extra"><br><div class=3D"gmail_quote"><div><div class=3D"h5">2015=
-06-01 23:14 GMT+07:00 Alexander Vowinkel <span dir=3D"ltr">&lt;<a href=3D"=
mailto:vowinkel.alexander@gmail.com" target=3D"_blank">vowinkel.alexander@g=
mail.com</a>&gt;</span>:<br></div></div><blockquote class=3D"gmail_quote" s=
tyle=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div=
><div class=3D"h5"><div dir=3D"ltr">Hi Team,<div><br></div><div>here is ano=
ther question:</div><div>Following code reads a fastq-file.</div><div>The f=
ile I&#39;m testing on has=C2=A0263333413 records:</div><div><blockquote cl=
ass=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px=
;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1e=
x">$ zcat C563WACXX_1.fastq.gz | wc -l<br>1053333652</blockquote></div><div=
><br></div><div>The problem is, that the code seems to only read</div><div>=
the first=C2=A04000000 records. I don&#39;t understand why.</div><div><br><=
/div><div>Can you advise me here?</div><div><br></div><div>Thank you,</div>=
<div>Alexander</div><div><br></div><div>PS: I removed try/catch for better =
readability</div><div><br><blockquote class=3D"gmail_quote" style=3D"margin=
:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204)=
;border-left-style:solid;padding-left:1ex">seqan::StringSet&lt;seqan::CharS=
tring&gt; ids;<br>seqan::StringSet&lt;seqan::Dna5QString&gt; seqs;<br>seqan=
::StringSet&lt;seqan::CharString&gt; quals;<br>unsigned batchSize =3D 10000=
;<br>do {<br>seqan::clear(ids);=C2=A0seqan::clear(seqs);=C2=A0seqan::clear(=
quals);<br>readRecords(ids, seqs, quals, inputFile, batchSize);<br>processR=
ecords(ids, seqs, quals, barcodeGraph, vertexFilePtrMap);<br>totalProcessed=
 +=3D seqan::length(ids);<br>std::cout &lt;&lt; &quot;\r&quot;;<br>std::cou=
t &lt;&lt; &quot;reads processed in total: &quot; &lt;&lt; totalProcessed;<=
br>std::cout.flush();<br>} while(seqan::length(ids) &gt; 0);</blockquote></=
div></div>
<br></div></div>_______________________________________________<br>
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<br></blockquote></div><br></div>
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From vowinkel.alexander@gmail.com Wed Jun 03 16:56:10 2015
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From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
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Subject: Re: [Seqan-dev] Infix of const String
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Hi Fadhlan,

your example also works for me.
The difference is, that you use as first parameter a DnaString.
I use representative(indexIt), which is according to the error message
a pointer to a Dna5String.
I would say that this should work as well.

Best,
Alexander

2015-06-02 23:42 GMT-05:00 Fadhlan Rizal <fadhlan.fari@gmail.com>:

> i don't know, but when i using my program it's work perfectly, of course =
i
> using another type (not TBarcodeString).
>
> here my example:
>
> DnaString mySekuens  =3D "ACGTACGTACGT";
>
> startPosition =3D 0;
> endPosition =3D startPosition + 5;
>
> Infix<String<Dna> >::Type inf;
> inf =3D infix(mySekuens, startPosition, endPosition);
>
>
> the output  ACGTA;
>
> 2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.co=
m
> >:
>
>> Hi Team,
>>
>> adopting from IndexIterators Tutorial, following problem came up:
>>
>> When I want to save an Infix of an representative in an Index Iterator:
>>
>> seqan::Infix<TBarcodeString>::Type referenceIfx =3D
>>> infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);
>>
>>
>> the error pops up, that I can't use a const String for this:
>>
>> /opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42:
>>> error: invalid conversion from =E2=80=98seqan::Pointer_<const
>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>> seqan::Alloc<> > >::Type {aka const
>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>> seqan::Alloc<> >*}=E2=80=99 to
>>> =E2=80=98seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char,
>>> seqan::Dna5_>, seqan::Alloc<> > >::Type {aka
>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>> seqan::Alloc<> >*}=E2=80=99 [-fpermissive]
>>>          data_host(_toPointer(host(_other))),
>>
>>
>> Solutions?
>>
>> Best,
>> Alexander
>>
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>
>>
>
> _______________________________________________
> seqan-dev mailing list
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<div dir=3D"ltr">Hi Fadhlan,<div><br></div><div>your example also works for=
 me.</div><div>The difference is, that you use as first parameter a=C2=A0<s=
pan style=3D"font-size:13px">DnaString.</span></div><div><span style=3D"fon=
t-size:13px">I use=C2=A0</span><span style=3D"font-size:12.8000001907349px"=
>representative(indexIt), which is according to the error message</span></d=
iv><div><span style=3D"font-size:12.8000001907349px">a pointer to a=C2=A0</=
span><span style=3D"font-size:13px">Dna5String.</span></div><div><span styl=
e=3D"font-size:13px">I would say that this should work as well.</span></div=
><div><span style=3D"font-size:13px"><br></span></div><div><span style=3D"f=
ont-size:13px">Best,</span></div><div><span style=3D"font-size:13px">Alexan=
der</span></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_qu=
ote">2015-06-02 23:42 GMT-05:00 Fadhlan Rizal <span dir=3D"ltr">&lt;<a href=
=3D"mailto:fadhlan.fari@gmail.com" target=3D"_blank">fadhlan.fari@gmail.com=
</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0=
 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr">i don&#=
39;t know, but when i using my program it&#39;s work perfectly, of course i=
 using another type (not=C2=A0<span style=3D"font-size:13px">TBarcodeString=
).</span><div><span style=3D"font-size:13px"><br></span></div><div><span st=
yle=3D"font-size:13px">here my example:</span></div><div><span style=3D"fon=
t-size:13px"><br></span></div><div><span style=3D"font-size:13px">DnaString=
 mySekuens =C2=A0=3D &quot;ACGTACGTACGT&quot;;</span></div><div><span style=
=3D"font-size:13px"><br></span></div><div><span style=3D"font-size:13px">st=
artPosition =3D 0;</span></div><div><span style=3D"font-size:13px">endPosit=
ion =3D startPosition + 5;</span></div><div><span style=3D"font-size:13px">=
<br></span></div><div>Infix&lt;String&lt;Dna&gt; &gt;::Type inf;<br></div><=
div>inf =3D infix(mySekuens, startPosition, endPosition);</div><div><br></d=
iv><div><br></div><div>the output =C2=A0<span style=3D"font-size:13px">ACGT=
A;</span></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quo=
te"><div><div class=3D"h5">2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <sp=
an dir=3D"ltr">&lt;<a href=3D"mailto:vowinkel.alexander@gmail.com" target=
=3D"_blank">vowinkel.alexander@gmail.com</a>&gt;</span>:<br></div></div><bl=
ockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #=
ccc solid;padding-left:1ex"><div><div class=3D"h5"><div dir=3D"ltr">Hi Team=
,<div><br></div><div>adopting from IndexIterators Tutorial, following probl=
em came up:</div><div><br></div><div>When I want to save an Infix of an rep=
resentative in an Index Iterator:</div><div><br></div><blockquote class=3D"=
gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border=
-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">seqa=
n::Infix&lt;TBarcodeString&gt;::Type referenceIfx =3D infix(representative(=
indexIt), parentRepLength(indexIt) + 1, endPos);</blockquote><div><br></div=
><div>the error pops up, that I can&#39;t use a const String for this:</div=
><div><br></div><div><blockquote class=3D"gmail_quote" style=3D"margin:0px =
0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);bord=
er-left-style:solid;padding-left:1ex">/opt/seqan/seqan-src/include/seqan/se=
quence/segment_infix.h:135:42: error: invalid conversion from =E2=80=98seqa=
n::Pointer_&lt;const seqan::String&lt;seqan::SimpleType&lt;unsigned char, s=
eqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt; &gt;::Type {aka const seqan::Str=
ing&lt;seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&l=
t;&gt; &gt;*}=E2=80=99 to =E2=80=98seqan::Pointer_&lt;seqan::String&lt;seqa=
n::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;=
 &gt;::Type {aka seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan=
::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=80=99 [-fpermissive]<br>=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0data_host(_toPointer(host(_other))),</blockquote=
><div><br></div><div>Solutions?</div><div><br></div><div>Best,</div><div>Al=
exander=C2=A0</div></div></div>
<br></div></div>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de">seqan-dev@lists.fu-berlin.d=
e</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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I'm new to Seqan and trying to create the suffix array from a large fa file
(~500MB) and search for a particular pattern. I am using the
"Index<Dna5String>" to create an index and "Finder" to create a finder
based on that index, am I doing right? Also, if I would like to store the
suffix array to hard disk what should I do?

Thanks!

--001a11379242ec09de0517a017d6
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<div dir=3D"ltr"><div>I&#39;m new to Seqan and trying to create the suffix =
array from a large fa file (~500MB) and search for a particular pattern. I =
am using the &quot;Index&lt;Dna5String&gt;&quot; to create an index and &qu=
ot;Finder&quot; to create a finder based on that index, am I doing right? A=
lso, if I would like to store the suffix array to hard disk what should I d=
o?=C2=A0</div><div><br></div><div>Thanks!</div></div>

--001a11379242ec09de0517a017d6--



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Hi,

did you read the Tutorial [1]?

In [2] it is shown how to search in an Index and how to store an Index on
HDD.

Best,
Alexander

[1] http://seqan.readthedocs.org/en/develop/Tutorial.html
[2] http://seqan.readthedocs.org/en/develop/Tutorial/Indices.html

2015-06-03 12:07 GMT-05:00 Yue Gan <gany.fml@gmail.com>:

> I'm new to Seqan and trying to create the suffix array from a large fa
> file (~500MB) and search for a particular pattern. I am using the
> "Index<Dna5String>" to create an index and "Finder" to create a finder
> based on that index, am I doing right? Also, if I would like to store the
> suffix array to hard disk what should I do?
>
> Thanks!
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
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<div dir=3D"ltr">Hi,<div><br></div><div>did you read the Tutorial [1]?</div=
><div><br></div><div>In [2] it is shown how to search in an Index and how t=
o store an Index on HDD.</div><div><br></div><div>Best,</div><div>Alexander=
</div><div><br></div><div>[1] <a href=3D"http://seqan.readthedocs.org/en/de=
velop/Tutorial.html">http://seqan.readthedocs.org/en/develop/Tutorial.html<=
/a></div><div>[2] <a href=3D"http://seqan.readthedocs.org/en/develop/Tutori=
al/Indices.html">http://seqan.readthedocs.org/en/develop/Tutorial/Indices.h=
tml</a></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote=
">2015-06-03 12:07 GMT-05:00 Yue Gan <span dir=3D"ltr">&lt;<a href=3D"mailt=
o:gany.fml@gmail.com" target=3D"_blank">gany.fml@gmail.com</a>&gt;</span>:<=
br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left=
:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div>I&#39;m new to Seqa=
n and trying to create the suffix array from a large fa file (~500MB) and s=
earch for a particular pattern. I am using the &quot;Index&lt;Dna5String&gt=
;&quot; to create an index and &quot;Finder&quot; to create a finder based =
on that index, am I doing right? Also, if I would like to store the suffix =
array to hard disk what should I do?=C2=A0</div><div><br></div><div>Thanks!=
</div></div>
<br>_______________________________________________<br>
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e</a><br>
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>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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From: Fadhlan Rizal <fadhlan.fari@gmail.com>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
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hi,
hmm, i never use that for pointer.
sorry i can't help you.

best regards.

2015-06-03 21:56 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.com=
>
:

> Hi Fadhlan,
>
> your example also works for me.
> The difference is, that you use as first parameter a DnaString.
> I use representative(indexIt), which is according to the error message
> a pointer to a Dna5String.
> I would say that this should work as well.
>
> Best,
> Alexander
>
> 2015-06-02 23:42 GMT-05:00 Fadhlan Rizal <fadhlan.fari@gmail.com>:
>
>> i don't know, but when i using my program it's work perfectly, of course
>> i using another type (not TBarcodeString).
>>
>> here my example:
>>
>> DnaString mySekuens  =3D "ACGTACGTACGT";
>>
>> startPosition =3D 0;
>> endPosition =3D startPosition + 5;
>>
>> Infix<String<Dna> >::Type inf;
>> inf =3D infix(mySekuens, startPosition, endPosition);
>>
>>
>> the output  ACGTA;
>>
>> 2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <
>> vowinkel.alexander@gmail.com>:
>>
>>> Hi Team,
>>>
>>> adopting from IndexIterators Tutorial, following problem came up:
>>>
>>> When I want to save an Infix of an representative in an Index Iterator:
>>>
>>> seqan::Infix<TBarcodeString>::Type referenceIfx =3D
>>>> infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);
>>>
>>>
>>> the error pops up, that I can't use a const String for this:
>>>
>>> /opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42:
>>>> error: invalid conversion from =E2=80=98seqan::Pointer_<const
>>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>>> seqan::Alloc<> > >::Type {aka const
>>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>>> seqan::Alloc<> >*}=E2=80=99 to
>>>> =E2=80=98seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char=
,
>>>> seqan::Dna5_>, seqan::Alloc<> > >::Type {aka
>>>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>>>> seqan::Alloc<> >*}=E2=80=99 [-fpermissive]
>>>>          data_host(_toPointer(host(_other))),
>>>
>>>
>>> Solutions?
>>>
>>> Best,
>>> Alexander
>>>
>>> _______________________________________________
>>> seqan-dev mailing list
>>> seqan-dev@lists.fu-berlin.de
>>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>>
>>>
>>
>> _______________________________________________
>> seqan-dev mailing list
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>>
>
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<div dir=3D"ltr">hi,<div>hmm, i never use that for pointer.</div><div>sorry=
 i can&#39;t help you.</div><div><br></div><div>best regards.</div></div><d=
iv class=3D"gmail_extra"><br><div class=3D"gmail_quote">2015-06-03 21:56 GM=
T+07:00 Alexander Vowinkel <span dir=3D"ltr">&lt;<a href=3D"mailto:vowinkel=
.alexander@gmail.com" target=3D"_blank">vowinkel.alexander@gmail.com</a>&gt=
;</span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;b=
order-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr">Hi Fadhlan,<di=
v><br></div><div>your example also works for me.</div><div>The difference i=
s, that you use as first parameter a=C2=A0<span style=3D"font-size:13px">Dn=
aString.</span></div><div><span style=3D"font-size:13px">I use=C2=A0</span>=
<span style=3D"font-size:12.8000001907349px">representative(indexIt), which=
 is according to the error message</span></div><div><span style=3D"font-siz=
e:12.8000001907349px">a pointer to a=C2=A0</span><span style=3D"font-size:1=
3px">Dna5String.</span></div><div><span style=3D"font-size:13px">I would sa=
y that this should work as well.</span></div><div><span style=3D"font-size:=
13px"><br></span></div><div><span style=3D"font-size:13px">Best,</span></di=
v><div><span style=3D"font-size:13px">Alexander</span></div></div><div clas=
s=3D"HOEnZb"><div class=3D"h5"><div class=3D"gmail_extra"><br><div class=3D=
"gmail_quote">2015-06-02 23:42 GMT-05:00 Fadhlan Rizal <span dir=3D"ltr">&l=
t;<a href=3D"mailto:fadhlan.fari@gmail.com" target=3D"_blank">fadhlan.fari@=
gmail.com</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" style=3D"mar=
gin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr=
">i don&#39;t know, but when i using my program it&#39;s work perfectly, of=
 course i using another type (not=C2=A0<span style=3D"font-size:13px">TBarc=
odeString).</span><div><span style=3D"font-size:13px"><br></span></div><div=
><span style=3D"font-size:13px">here my example:</span></div><div><span sty=
le=3D"font-size:13px"><br></span></div><div><span style=3D"font-size:13px">=
DnaString mySekuens =C2=A0=3D &quot;ACGTACGTACGT&quot;;</span></div><div><s=
pan style=3D"font-size:13px"><br></span></div><div><span style=3D"font-size=
:13px">startPosition =3D 0;</span></div><div><span style=3D"font-size:13px"=
>endPosition =3D startPosition + 5;</span></div><div><span style=3D"font-si=
ze:13px"><br></span></div><div>Infix&lt;String&lt;Dna&gt; &gt;::Type inf;<b=
r></div><div>inf =3D infix(mySekuens, startPosition, endPosition);</div><di=
v><br></div><div><br></div><div>the output =C2=A0<span style=3D"font-size:1=
3px">ACGTA;</span></div></div><div class=3D"gmail_extra"><br><div class=3D"=
gmail_quote"><div><div>2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <span d=
ir=3D"ltr">&lt;<a href=3D"mailto:vowinkel.alexander@gmail.com" target=3D"_b=
lank">vowinkel.alexander@gmail.com</a>&gt;</span>:<br></div></div><blockquo=
te class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc so=
lid;padding-left:1ex"><div><div><div dir=3D"ltr">Hi Team,<div><br></div><di=
v>adopting from IndexIterators Tutorial, following problem came up:</div><d=
iv><br></div><div>When I want to save an Infix of an representative in an I=
ndex Iterator:</div><div><br></div><blockquote class=3D"gmail_quote" style=
=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(20=
4,204,204);border-left-style:solid;padding-left:1ex">seqan::Infix&lt;TBarco=
deString&gt;::Type referenceIfx =3D infix(representative(indexIt), parentRe=
pLength(indexIt) + 1, endPos);</blockquote><div><br></div><div>the error po=
ps up, that I can&#39;t use a const String for this:</div><div><br></div><d=
iv><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;bord=
er-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:soli=
d;padding-left:1ex">/opt/seqan/seqan-src/include/seqan/sequence/segment_inf=
ix.h:135:42: error: invalid conversion from =E2=80=98seqan::Pointer_&lt;con=
st seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, s=
eqan::Alloc&lt;&gt; &gt; &gt;::Type {aka const seqan::String&lt;seqan::Simp=
leType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=
=80=99 to =E2=80=98seqan::Pointer_&lt;seqan::String&lt;seqan::SimpleType&lt=
;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt; &gt;::Type {aka=
 seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seq=
an::Alloc&lt;&gt; &gt;*}=E2=80=99 [-fpermissive]<br>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0data_host(_toPointer(host(_other))),</blockquote><div><br></di=
v><div>Solutions?</div><div><br></div><div>Best,</div><div>Alexander=C2=A0<=
/div></div></div>
<br></div></div>_______________________________________________<br>
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@lists.fu-berlin.de</a><br>
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>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
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<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
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From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
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Subject: Re: [Seqan-dev] Infix of const String
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Indeed!

More to find there: https://github.com/seqan/seqan/issues/1009

2015-06-04 13:53 GMT-05:00 Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de>:

>  Hi Alexander,
>
>  it seems to me that the error message complains about a const to
> non-const type cast.
> The function representative returns a pointer to a const String, while yo=
u
> are trying to assign this to an pointer to non-const String.
> So I guess
>
>  typename Infix<TBarcodeString const>::Type would solve the compiler
> error?
> Can you please try this?
>
>  Cheers,
>
>  Ren=C3=A9
>
>  On 03 Jun 2015, at 01:46, Alexander Vowinkel <
> vowinkel.alexander@gmail.com> wrote:
>
>  Hi Team,
>
>  adopting from IndexIterators Tutorial, following problem came up:
>
>  When I want to save an Infix of an representative in an Index Iterator:
>
>  seqan::Infix<TBarcodeString>::Type referenceIfx =3D
>> infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);
>
>
>  the error pops up, that I can't use a const String for this:
>
>   /opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42:
>> error: invalid conversion from =E2=80=98seqan::Pointer_<const
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> > >::Type {aka const
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> >*}=E2=80=99 to
>> =E2=80=98seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char,
>> seqan::Dna5_>, seqan::Alloc<> > >::Type {aka
>> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
>> seqan::Alloc<> >*}=E2=80=99 [-fpermissive]
>>          data_host(_toPointer(host(_other))),
>
>
>  Solutions?
>
>  Best,
> Alexander
>  _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>
>  ---
>
>  Ren=C3=A9 Rahn
> Ph.D. Student
> --------------------------------
>  Tel:  (+49) 30 838 75137
> Mail: rene.rahn@fu-berlin.de
> --------------------------------
>  Institute of Computer Science
> Algorithmic Bioinformatics (ABI)
> --------------------------------
> Freie Universit=C3=A4t Berlin
> Takustra=C3=9Fe 9
> 14195 Berlin
> --------------------------------
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

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<div dir=3D"ltr">Indeed!<div><br></div><div>More to find there:=C2=A0<a hre=
f=3D"https://github.com/seqan/seqan/issues/1009">https://github.com/seqan/s=
eqan/issues/1009</a></div></div><div class=3D"gmail_extra"><br><div class=
=3D"gmail_quote">2015-06-04 13:53 GMT-05:00 Rahn, Ren=C3=A9 <span dir=3D"lt=
r">&lt;<a href=3D"mailto:rene.maerker@fu-berlin.de" target=3D"_blank">rene.=
maerker@fu-berlin.de</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" s=
tyle=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style=3D"word-wrap:break-word">
Hi Alexander,
<div><br>
</div>
<div>it seems to me that the error message complains about a const to non-c=
onst type cast.=C2=A0</div>
<div>The function representative returns a pointer to a const String, while=
 you are trying to assign this to an pointer to non-const String.</div>
<div>So I guess=C2=A0</div>
<div><br>
</div>
<div>typename Infix&lt;TBarcodeString const&gt;::Type would solve the compi=
ler error?</div>
<div>Can you please try this?</div>
<div><br>
</div>
<div>Cheers,=C2=A0</div>
<div><br>
</div>
<div>Ren=C3=A9</div>
<div><br>
<div>
<blockquote type=3D"cite"><div><div class=3D"h5">
<div>On 03 Jun 2015, at 01:46, Alexander Vowinkel &lt;<a href=3D"mailto:vow=
inkel.alexander@gmail.com" target=3D"_blank">vowinkel.alexander@gmail.com</=
a>&gt; wrote:</div>
<br>
</div></div><div><div><div class=3D"h5">
<div dir=3D"ltr">Hi Team,
<div><br>
</div>
<div>adopting from IndexIterators Tutorial, following problem came up:</div=
>
<div><br>
</div>
<div>When I want to save an Infix of an representative in an Index Iterator=
:</div>
<div><br>
</div>
<blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-=
left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;p=
adding-left:1ex">
seqan::Infix&lt;TBarcodeString&gt;::Type referenceIfx =3D infix(representat=
ive(indexIt), parentRepLength(indexIt) + 1, endPos);</blockquote>
<div><br>
</div>
<div>the error pops up, that I can&#39;t use a const String for this:</div>
<div><br>
</div>
<div>
<blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-=
left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;p=
adding-left:1ex">
/opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42: error: =
invalid conversion from =E2=80=98seqan::Pointer_&lt;const seqan::String&lt;=
seqan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; =
&gt; &gt;::Type {aka const seqan::String&lt;seqan::SimpleType&lt;unsigned
 char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt;*}=E2=80=99 to =E2=80=98s=
eqan::Pointer_&lt;seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqa=
n::Dna5_&gt;, seqan::Alloc&lt;&gt; &gt; &gt;::Type {aka seqan::String&lt;se=
qan::SimpleType&lt;unsigned char, seqan::Dna5_&gt;, seqan::Alloc&lt;&gt; &g=
t;*}=E2=80=99 [-fpermissive]<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0data_host(_toPointer(host(_other))),</blo=
ckquote>
<div><br>
</div>
<div>Solutions?</div>
<div><br>
</div>
<div>Best,</div>
<div>Alexander=C2=A0</div>
</div>
</div></div></div><span class=3D"">
_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
</span></div>
</blockquote>
</div>
<br>
<div>
<div style=3D"color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wra=
p:break-word">
<div><font face=3D"Courier New">---</font></div>
<div><font face=3D"Courier New"><br>
</font></div>
<div><font face=3D"Courier New">Ren=C3=A9 Rahn</font></div>
<div><font face=3D"Courier New">Ph.D. Student</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div>
<div><font face=3D"Courier New">Tel: =C2=A0(+49) 30 838 75137</font></div>
<div><font face=3D"Courier New">Mail:=C2=A0<a href=3D"mailto:rene.rahn@fu-b=
erlin.de" target=3D"_blank">rene.rahn@fu-berlin.de</a></font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
<div><font face=3D"Courier New">Institute of Computer Science</font></div>
<div><font face=3D"Courier New">Algorithmic Bioinformatics (ABI)</font></di=
v>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div><font face=3D"Courier New">Freie Universit=C3=A4t Berlin</font></div>
<div><font face=3D"Courier New">Takustra=C3=9Fe 9</font></div>
<div><font face=3D"Courier New">14195 Berlin</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
</div>
<br>
</div>
</div>

<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de">seqan-dev@lists.fu-berlin.d=
e</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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From: Brett Bowman <bnbowman@gmail.com>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
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Subject: Re: [Seqan-dev] Asymmetric Scoring of Insertions / Deletions in
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Thanks Rene,

That appears to let me create the type of scoring schemes I need, but it
looks like "computeAlignmentStats" function can't quite handle the
polymorphism yet:

"""
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/src/ControlFilter.cpp:50:
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/include/pbsparse/FindSeedsConfig.h:40:
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align.h:55:
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/graph_align.=
h:45:
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score.h:49:
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score/score_=
simple.h:224:15:
error: no member
      named 'data_gap_open' in 'seqan::Score<long, const
seqan::Tag<seqan::BiAffine_> >'
    return me.data_gap_open;
           ~~ ^
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align/evalua=
te_alignment.h:227:41:
note: in
      instantiation of function template specialization
'seqan::scoreGapOpen<long, const seqan::Tag<seqan::BiAffine_> >' requested
here
                stats.alignmentScore +=3D scoreGapOpen(scoringScheme);
                                        ^
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/include/pbsparse/BandedAligner.h:300:9:
note: in instantiation of function template
      specialization
'seqan::computeAlignmentStats<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>,
long, const
      seqan::Tag<seqan::BiAffine_> >' requested here
        computeAlignmentStats(stats, align, scoringScheme_);
"""

-B

On Wed, Jun 3, 2015 at 8:21 AM, Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de>
wrote:

>  Hi Brett,
>
>  this is possible with the BiAffine Score specification.
> However this was so far only used in the JournaledStringSet module which
> is still under development.
> You can access it by simply including
> <seqan/journaled_set/score_biaffine.h>
>
>  You can use the setter and getter functions:
>
>  setScore/score
> setScoreMismatch/scoreMismatch
> setScoreGapOpenVertical/scoreGapOpenVertical
> setScoreGapOpenHorizontal/scoreGapOpenHorizontal
> and of course the standard setGap interfaces.
>
>  Apart from this, the entire align engine for the standard DP algorithms
> works with different gap penalties for insertions/deletions.
>
>  Cheers,
>
>  Ren=C3=A9
>
>
>
>  On 26 May 2015, at 23:57, Brett Bowman <bnbowman@gmail.com> wrote:
>
>  I'd like to create some scoring schemes with asymmetric weights for
> insertion / deletion errors for working with single-molecule sequencing
> data.  Raw data from both PacBio and Oxford Nanopore have known
> insertion-biases, and so optimal scoring schemes need to penalize those
> errors less than deletions.
>
>  This appears to be partially supported by the SeqAn API already, since
> the "Score" class has separate interface functions for "scoreGapHorizonta=
l"
> and "scoreGapVertical", but I can't see any existing specifications that
> utilize them.
>
>  Is there an allowed / recommended way to do this currently, or do I need
> to create my own Score specialization?
>
>  Sincerely,
> -Brett
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>
>  ---
>
>  Ren=C3=A9 Rahn
> Ph.D. Student
> --------------------------------
>  Tel:  (+49) 30 838 75137
> Mail: rene.rahn@fu-berlin.de
> --------------------------------
>  Institute of Computer Science
> Algorithmic Bioinformatics (ABI)
> --------------------------------
> Freie Universit=C3=A4t Berlin
> Takustra=C3=9Fe 9
> 14195 Berlin
> --------------------------------
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

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<div dir=3D"ltr">Thanks Rene,<div><br></div><div>That appears to let me cre=
ate the type of scoring schemes I need, but it looks like &quot;computeAlig=
nmentStats&quot; function can&#39;t quite handle the polymorphism yet:</div=
><div><br></div><div>&quot;&quot;&quot;<br></div><div><div>In file included=
 from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/stagin=
g/PostPrimary/pbsparse/src/ControlFilter.cpp:50:</div><div>In file included=
 from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/stagin=
g/PostPrimary/pbsparse/include/pbsparse/FindSeedsConfig.h:40:</div><div>In =
file included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinfor=
matics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include=
/seqan/align.h:55:</div><div>In file included from /home/UNIXHOME/bbowman/p=
4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-p=
arty/seqan-library-2.0.0/include/seqan/graph_align.h:45:</div><div>In file =
included from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatic=
s/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqa=
n/score.h:49:</div><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bio=
informatics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/in=
clude/seqan/score/score_simple.h:224:15: error: no member</div><div>=C2=A0 =
=C2=A0 =C2=A0 named &#39;data_gap_open&#39; in &#39;seqan::Score&lt;long, c=
onst seqan::Tag&lt;seqan::BiAffine_&gt; &gt;&#39;</div><div>=C2=A0 =C2=A0 r=
eturn me.data_gap_open;</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
~~ ^</div><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformati=
cs/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seq=
an/align/evaluate_alignment.h:227:41: note: in</div><div>=C2=A0 =C2=A0 =C2=
=A0 instantiation of function template specialization &#39;seqan::scoreGapO=
pen&lt;long, const seqan::Tag&lt;seqan::BiAffine_&gt; &gt;&#39; requested h=
ere</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 stats=
.alignmentScore +=3D scoreGapOpen(scoringScheme);</div><div>=C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^</div><div>/home/UNIX=
HOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pb=
sparse/include/pbsparse/BandedAligner.h:300:9: note: in instantiation of fu=
nction template</div><div>=C2=A0 =C2=A0 =C2=A0 specialization &#39;seqan::c=
omputeAlignmentStats&lt;seqan::String&lt;seqan::SimpleType&lt;unsigned char=
, seqan::Dna_&gt;, seqan::Alloc&lt;void&gt; &gt;, seqan::Tag&lt;seqan::Arra=
yGaps_&gt;, long, const</div><div>=C2=A0 =C2=A0 =C2=A0 seqan::Tag&lt;seqan:=
:BiAffine_&gt; &gt;&#39; requested here</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 computeAlignmentStats(stats, align, scoringScheme_);</div></div><div>&q=
uot;&quot;&quot;</div><div><br></div><div>-B</div><img src=3D"http://t.sigo=
pn03.com/e1t/o/5/f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v4fhjlVRzvbY8qSQGCVRz=
H2b1pctGFW4bXls31k1H6H0?si=3D4738980717789184&amp;pi=3Dd2362f3f-4a05-4259-c=
422-e7d270b1d0a3" style=3D"display:none!important" height=3D"1" width=3D"1"=
></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Wed, Ju=
n 3, 2015 at 8:21 AM, Rahn, Ren=C3=A9 <span dir=3D"ltr">&lt;<a href=3D"mail=
to:rene.maerker@fu-berlin.de" target=3D"_blank">rene.maerker@fu-berlin.de</=
a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0=
 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style=3D"word-wrap:break-word">
Hi Brett,=C2=A0
<div><br>
</div>
<div>this is possible with the BiAffine Score specification.</div>
<div>However this was so far only used in the JournaledStringSet module whi=
ch is still under development.</div>
<div>You can access it by simply including &lt;seqan/journaled_set/score_bi=
affine.h&gt;</div>
<div><br>
</div>
<div>You can use the setter and getter functions:</div>
<div><br>
</div>
<div>setScore/score</div>
<div>setScoreMismatch/scoreMismatch</div>
<div>setScoreGapOpenVertical/scoreGapOpenVertical</div>
<div>setScoreGapOpenHorizontal/scoreGapOpenHorizontal</div>
<div>and of course the standard setGap interfaces.</div>
<div><br>
</div>
<div>Apart from this, the entire align engine for the standard DP algorithm=
s works with different gap penalties for insertions/deletions.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Ren=C3=A9</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type=3D"cite"><div><div class=3D"h5">
<div>On 26 May 2015, at 23:57, Brett Bowman &lt;<a href=3D"mailto:bnbowman@=
gmail.com" target=3D"_blank">bnbowman@gmail.com</a>&gt; wrote:</div>
<br>
</div></div><div><div><div class=3D"h5">
<div dir=3D"ltr">
<div>I&#39;d like to create some scoring schemes with asymmetric weights fo=
r insertion / deletion errors for working with single-molecule sequencing d=
ata.=C2=A0 Raw data from both PacBio and Oxford Nanopore have known inserti=
on-biases, and so optimal scoring
 schemes need to penalize those errors less than deletions.=C2=A0</div>
<div><br>
</div>
<div>This appears to be partially supported by the SeqAn API already, since=
 the &quot;Score&quot; class has separate interface functions for &quot;sco=
reGapHorizontal&quot; and &quot;scoreGapVertical&quot;, but I can&#39;t see=
 any existing specifications that utilize them.</div>
<div><br>
</div>
<div>Is there an allowed / recommended way to do this currently, or do I ne=
ed to create my own Score specialization?</div>
<div><br>
</div>
<div>Sincerely,</div>
-Brett</div></div></div>
_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
</div>
</blockquote>
</div>
<br>
<div>
<div style=3D"color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wra=
p:break-word">
<div><font face=3D"Courier New">---</font></div>
<div><font face=3D"Courier New"><br>
</font></div>
<div><font face=3D"Courier New">Ren=C3=A9 Rahn</font></div>
<div><font face=3D"Courier New">Ph.D. Student</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div>
<div><font face=3D"Courier New">Tel: =C2=A0<a href=3D"tel:%28%2B49%29%2030%=
20838%2075137" value=3D"+493083875137" target=3D"_blank">(+49) 30 838 75137=
</a></font></div>
<div><font face=3D"Courier New">Mail:=C2=A0<a href=3D"mailto:rene.rahn@fu-b=
erlin.de" target=3D"_blank">rene.rahn@fu-berlin.de</a></font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
<div><font face=3D"Courier New">Institute of Computer Science</font></div>
<div><font face=3D"Courier New">Algorithmic Bioinformatics (ABI)</font></di=
v>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div><font face=3D"Courier New">Freie Universit=C3=A4t Berlin</font></div>
<div><font face=3D"Courier New">Takustra=C3=9Fe 9</font></div>
<div><font face=3D"Courier New">14195 Berlin</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
</div>
<br>
</div>
</div>

<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de">seqan-dev@lists.fu-berlin.d=
e</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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From: Brett Bowman <bnbowman@gmail.com>
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Trying to effect a patch to resolve this issue, but it appears that the
BiAffine scoreGap functions require the sequence bases in question for the
appropriate functions, despite not using them in the computation except for
match/mismatch.

Is this the intended design?

"""
template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
inline TScoreValue
scoreGapExtendVertical(Score<TScoreValue, BiAffine> const & me,
                       TSeqEntry1 const & /*seqEntry1*/,
                       TSeqEntry2 const & /*seqEntry2*/)
{
    return me._gapExtendVertical;
}
"""

-Brett

On Fri, Jun 5, 2015 at 10:39 AM, Brett Bowman <bnbowman@gmail.com> wrote:

> Thanks Rene,
>
> That appears to let me create the type of scoring schemes I need, but it
> looks like "computeAlignmentStats" function can't quite handle the
> polymorphism yet:
>
> """
> In file included from
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/src/ControlFilter.cpp:50:
> In file included from
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/include/pbsparse/FindSeedsConfig.h:40:
> In file included from
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align.h:55=
:
> In file included from
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/graph_alig=
n.h:45:
> In file included from
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score.h:49=
:
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/score/scor=
e_simple.h:224:15:
> error: no member
>       named 'data_gap_open' in 'seqan::Score<long, const
> seqan::Tag<seqan::BiAffine_> >'
>     return me.data_gap_open;
>            ~~ ^
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/align/eval=
uate_alignment.h:227:41:
> note: in
>       instantiation of function template specialization
> 'seqan::scoreGapOpen<long, const seqan::Tag<seqan::BiAffine_> >' requeste=
d
> here
>                 stats.alignmentScore +=3D scoreGapOpen(scoringScheme);
>                                         ^
> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Po=
stPrimary/pbsparse/include/pbsparse/BandedAligner.h:300:9:
> note: in instantiation of function template
>       specialization
> 'seqan::computeAlignmentStats<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>,
> long, const
>       seqan::Tag<seqan::BiAffine_> >' requested here
>         computeAlignmentStats(stats, align, scoringScheme_);
> """
>
> -B
>
> On Wed, Jun 3, 2015 at 8:21 AM, Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.d=
e>
> wrote:
>
>>  Hi Brett,
>>
>>  this is possible with the BiAffine Score specification.
>> However this was so far only used in the JournaledStringSet module which
>> is still under development.
>> You can access it by simply including
>> <seqan/journaled_set/score_biaffine.h>
>>
>>  You can use the setter and getter functions:
>>
>>  setScore/score
>> setScoreMismatch/scoreMismatch
>> setScoreGapOpenVertical/scoreGapOpenVertical
>> setScoreGapOpenHorizontal/scoreGapOpenHorizontal
>> and of course the standard setGap interfaces.
>>
>>  Apart from this, the entire align engine for the standard DP algorithms
>> works with different gap penalties for insertions/deletions.
>>
>>  Cheers,
>>
>>  Ren=C3=A9
>>
>>
>>
>>  On 26 May 2015, at 23:57, Brett Bowman <bnbowman@gmail.com> wrote:
>>
>>  I'd like to create some scoring schemes with asymmetric weights for
>> insertion / deletion errors for working with single-molecule sequencing
>> data.  Raw data from both PacBio and Oxford Nanopore have known
>> insertion-biases, and so optimal scoring schemes need to penalize those
>> errors less than deletions.
>>
>>  This appears to be partially supported by the SeqAn API already, since
>> the "Score" class has separate interface functions for "scoreGapHorizont=
al"
>> and "scoreGapVertical", but I can't see any existing specifications that
>> utilize them.
>>
>>  Is there an allowed / recommended way to do this currently, or do I
>> need to create my own Score specialization?
>>
>>  Sincerely,
>> -Brett
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>
>>
>>  ---
>>
>>  Ren=C3=A9 Rahn
>> Ph.D. Student
>> --------------------------------
>>  Tel:  (+49) 30 838 75137
>> Mail: rene.rahn@fu-berlin.de
>> --------------------------------
>>  Institute of Computer Science
>> Algorithmic Bioinformatics (ABI)
>> --------------------------------
>> Freie Universit=C3=A4t Berlin
>> Takustra=C3=9Fe 9
>> 14195 Berlin
>> --------------------------------
>>
>>
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>
>>
>

--047d7bfcf13a660e640517c90be6
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Trying to effect a patch to resolve this issue, but it app=
ears that the BiAffine scoreGap functions require the sequence bases in que=
stion for the appropriate functions, despite not using them in the computat=
ion except for match/mismatch.<div><br></div><div>Is this the intended desi=
gn?<br><div><br></div><div>&quot;&quot;&quot;</div><div><div>template &lt;t=
ypename TScoreValue, typename TSeqEntry1, typename TSeqEntry2&gt;</div><div=
>inline TScoreValue</div><div>scoreGapExtendVertical(Score&lt;TScoreValue, =
BiAffine&gt; const &amp; me,</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TSeqEntry1 const &amp; /*se=
qEntry1*/,</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0TSeqEntry2 const &amp; /*seqEntry2*/)</div><=
div>{</div><div>=C2=A0 =C2=A0 return me._gapExtendVertical;</div><div>}</di=
v></div><div>&quot;&quot;&quot;<br></div><div><br></div><div>-Brett</div></=
div><img src=3D"http://t.sigopn03.com/e1t/o/5/f18dQhb0S7ks8dDMPbW2n0x6l2B9g=
XrN7sKj6v4fhjlVRzvbY8qSQGCVRzH2b1pctGFW4bXls31k1H6H0?si=3D4738980717789184&=
amp;pi=3D3df4a765-63ca-4719-bcf4-b8c6312fa6c1" style=3D"display:none!import=
ant" height=3D"1" width=3D"1"></div><div class=3D"gmail_extra"><br><div cla=
ss=3D"gmail_quote">On Fri, Jun 5, 2015 at 10:39 AM, Brett Bowman <span dir=
=3D"ltr">&lt;<a href=3D"mailto:bnbowman@gmail.com" target=3D"_blank">bnbowm=
an@gmail.com</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" sty=
le=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div d=
ir=3D"ltr">Thanks Rene,<div><br></div><div>That appears to let me create th=
e type of scoring schemes I need, but it looks like &quot;computeAlignmentS=
tats&quot; function can&#39;t quite handle the polymorphism yet:</div><div>=
<br></div><div>&quot;&quot;&quot;<br></div><div><div>In file included from =
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/src/ControlFilter.cpp:50:</div><div>In file included from =
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/pbsparse/include/pbsparse/FindSeedsConfig.h:40:</div><div>In file i=
ncluded from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics=
/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan=
/align.h:55:</div><div>In file included from /home/UNIXHOME/bbowman/p4/soft=
ware/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/third-party/s=
eqan-library-2.0.0/include/seqan/graph_align.h:45:</div><div>In file includ=
ed from /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/stag=
ing/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/scor=
e.h:49:</div><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinform=
atics/staging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/=
seqan/score/score_simple.h:224:15: error: no member</div><div>=C2=A0 =C2=A0=
 =C2=A0 named &#39;data_gap_open&#39; in &#39;seqan::Score&lt;long, const s=
eqan::Tag&lt;seqan::BiAffine_&gt; &gt;&#39;</div><div>=C2=A0 =C2=A0 return =
me.data_gap_open;</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0~~ ^</=
div><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/sta=
ging/PostPrimary/pbsparse/third-party/seqan-library-2.0.0/include/seqan/ali=
gn/evaluate_alignment.h:227:41: note: in</div><div>=C2=A0 =C2=A0 =C2=A0 ins=
tantiation of function template specialization &#39;seqan::scoreGapOpen&lt;=
long, const seqan::Tag&lt;seqan::BiAffine_&gt; &gt;&#39; requested here</di=
v><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 stats.alignm=
entScore +=3D scoreGapOpen(scoringScheme);</div><div>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^</div><div>/home/UNIXHOME/bb=
owman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/pbsparse/=
include/pbsparse/BandedAligner.h:300:9: note: in instantiation of function =
template</div><div>=C2=A0 =C2=A0 =C2=A0 specialization &#39;seqan::computeA=
lignmentStats&lt;seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan=
::Dna_&gt;, seqan::Alloc&lt;void&gt; &gt;, seqan::Tag&lt;seqan::ArrayGaps_&=
gt;, long, const</div><div>=C2=A0 =C2=A0 =C2=A0 seqan::Tag&lt;seqan::BiAffi=
ne_&gt; &gt;&#39; requested here</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 comp=
uteAlignmentStats(stats, align, scoringScheme_);</div></div><div>&quot;&quo=
t;&quot;</div><div><br></div><div>-B</div></div><div class=3D"gmail_extra">=
<br><div class=3D"gmail_quote"><span class=3D"">On Wed, Jun 3, 2015 at 8:21=
 AM, Rahn, Ren=C3=A9 <span dir=3D"ltr">&lt;<a href=3D"mailto:rene.maerker@f=
u-berlin.de" target=3D"_blank">rene.maerker@fu-berlin.de</a>&gt;</span> wro=
te:<br></span><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;=
border-left:1px #ccc solid;padding-left:1ex">



<div style=3D"word-wrap:break-word"><span class=3D"">
Hi Brett,=C2=A0
<div><br>
</div>
<div>this is possible with the BiAffine Score specification.</div>
<div>However this was so far only used in the JournaledStringSet module whi=
ch is still under development.</div>
<div>You can access it by simply including &lt;seqan/journaled_set/score_bi=
affine.h&gt;</div>
<div><br>
</div>
<div>You can use the setter and getter functions:</div>
<div><br>
</div>
<div>setScore/score</div>
<div>setScoreMismatch/scoreMismatch</div>
<div>setScoreGapOpenVertical/scoreGapOpenVertical</div>
<div>setScoreGapOpenHorizontal/scoreGapOpenHorizontal</div>
<div>and of course the standard setGap interfaces.</div>
<div><br>
</div>
<div>Apart from this, the entire align engine for the standard DP algorithm=
s works with different gap penalties for insertions/deletions.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Ren=C3=A9</div>
<div><br>
</div>
<div><br>
</div>
</span><div><br>
<div>
<blockquote type=3D"cite"><span class=3D""><div><div>
<div>On 26 May 2015, at 23:57, Brett Bowman &lt;<a href=3D"mailto:bnbowman@=
gmail.com" target=3D"_blank">bnbowman@gmail.com</a>&gt; wrote:</div>
<br>
</div></div></span><div><span class=3D""><div><div>
<div dir=3D"ltr">
<div>I&#39;d like to create some scoring schemes with asymmetric weights fo=
r insertion / deletion errors for working with single-molecule sequencing d=
ata.=C2=A0 Raw data from both PacBio and Oxford Nanopore have known inserti=
on-biases, and so optimal scoring
 schemes need to penalize those errors less than deletions.=C2=A0</div>
<div><br>
</div>
<div>This appears to be partially supported by the SeqAn API already, since=
 the &quot;Score&quot; class has separate interface functions for &quot;sco=
reGapHorizontal&quot; and &quot;scoreGapVertical&quot;, but I can&#39;t see=
 any existing specifications that utilize them.</div>
<div><br>
</div>
<div>Is there an allowed / recommended way to do this currently, or do I ne=
ed to create my own Score specialization?</div>
<div><br>
</div>
<div>Sincerely,</div>
-Brett</div></div></div></span><span class=3D"">
_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
</span></div>
</blockquote>
</div><span class=3D"">
<br>
<div>
<div style=3D"color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wra=
p:break-word">
<div><font face=3D"Courier New">---</font></div>
<div><font face=3D"Courier New"><br>
</font></div>
<div><font face=3D"Courier New">Ren=C3=A9 Rahn</font></div>
<div><font face=3D"Courier New">Ph.D. Student</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div>
<div><font face=3D"Courier New">Tel: =C2=A0<a href=3D"tel:%28%2B49%29%2030%=
20838%2075137" value=3D"+493083875137" target=3D"_blank">(+49) 30 838 75137=
</a></font></div>
<div><font face=3D"Courier New">Mail:=C2=A0<a href=3D"mailto:rene.rahn@fu-b=
erlin.de" target=3D"_blank">rene.rahn@fu-berlin.de</a></font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
<div><font face=3D"Courier New">Institute of Computer Science</font></div>
<div><font face=3D"Courier New">Algorithmic Bioinformatics (ABI)</font></di=
v>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div><font face=3D"Courier New">Freie Universit=C3=A4t Berlin</font></div>
<div><font face=3D"Courier New">Takustra=C3=9Fe 9</font></div>
<div><font face=3D"Courier New">14195 Berlin</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
</div>
<br>
</span></div>
</div><span class=3D"">

<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></span></blockquote></div><br></div>
</blockquote></div><br></div>

--047d7bfcf13a660e640517c90be6--



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Subject: [Seqan-dev] Cannonical Alignment Row Ordering
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Is there a standardized way to order sequences in Alignment objects in
SeqAn?

Reason being that the code in "align/evalulate_alignment.h" appears to take
Row #0 as the reference:
"""
    // Get iterators.
    TGapsIter it0 = begin(row(align, 0));
    TGapsIter itEnd0 = end(row(align, 0));
    TGapsIter it1 = begin(row(align, 1));
    TGapsIter itEnd1 = end(row(align, 1));

    for (; it0 != itEnd0 && it1 != itEnd1; ++it0, ++it1)
    {
        if (isGap(it0))
        {
            stats.numDeletions += 1;
        }

        if (isGap(it1))
        {
            stats.numInsertions += 1;
        }
   }
"""

While the code for writing alignments in "align/align_base.h" prints rows
in numerical order, which puts the query below the reference, in an
inversion of standard practice:
"""
  Reference ATCTCTCTC-A-ACAACAA--CAACGGAGGAGG-AGGAAAAGAGAGAGAT
  Align        |||||||||*|*|||||||**||||||||||||*||||||||||||||||
  Query      ATCTCTCTCAACACAACAACGCAACGGAGGAGGAAGGAAAAGAGAGAGAT
"""

I think this also runs counter to how a number of SDP algorithms are
traditional written, where seqan puts the Horizontal sequence first, which
IIRC is traditionally the query not the reference (e.g. Baker & Giancarlo
(2002), http://www.sciencedirect.com/science/article/pii/S0196677402912149)
"""
    assignSource(row(alignment, 0), sequenceH);
    assignSource(row(alignment, 1), sequenceV);

    Score<int, Simple> scoringScheme(2, -1, -2);

    int result = bandedChainAlignment(alignment, seedChain, scoringScheme,
2);
"""

-Brett

--047d7b5d848de2448c0517c9b938
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<div dir=3D"ltr"><div>Is there a standardized way to order sequences in Ali=
gnment objects in SeqAn?</div><div><br></div><div>Reason being that the cod=
e in &quot;align/evalulate_alignment.h&quot; appears to take Row #0 as the =
reference:</div><div>&quot;&quot;&quot;</div><div><div><div>=C2=A0 =C2=A0 /=
/ Get iterators.</div><div>=C2=A0 =C2=A0 TGapsIter it0 =3D begin(row(align,=
 0));</div><div>=C2=A0 =C2=A0 TGapsIter itEnd0 =3D end(row(align, 0));</div=
><div>=C2=A0 =C2=A0 TGapsIter it1 =3D begin(row(align, 1));</div><div>=C2=
=A0 =C2=A0 TGapsIter itEnd1 =3D end(row(align, 1));</div><div><br></div><di=
v>=C2=A0 =C2=A0 for (; it0 !=3D itEnd0 &amp;&amp; it1 !=3D itEnd1; ++it0, +=
+it1)</div><div>=C2=A0 =C2=A0 {</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 if (i=
sGap(it0))</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 {</div><div>=C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 stats.numDeletions +=3D 1;<br></div><div>=C2=A0=
 =C2=A0 =C2=A0 =C2=A0 }<br></div><div><br></div><div>=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 if (isGap(it1))</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 {</div><div>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 stats.numInsertions +=3D 1;<br></=
div><div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 }<br></div></div><div>=C2=A0 =C2=A0}</=
div></div><div>&quot;&quot;&quot;<br></div><div><br></div><div>While the co=
de for writing alignments in &quot;align/align_base.h&quot; prints rows in =
numerical order, which puts the query below the reference, in an inversion =
of standard practice:</div><div>&quot;&quot;&quot;</div><div><div>=C2=A0 Re=
ference ATCTCTCTC-A-ACAACAA--CAACGGAGGAGG-AGGAAAAGAGAGAGAT</div><div>=C2=A0=
 Align =C2=A0 =C2=A0 =C2=A0 =C2=A0|||||||||*|*|||||||**||||||||||||*|||||||=
|||||||||</div><div>=C2=A0 Query =C2=A0 =C2=A0 =C2=A0ATCTCTCTCAACACAACAACGC=
AACGGAGGAGGAAGGAAAAGAGAGAGAT</div></div><div>&quot;&quot;&quot;<br></div><d=
iv><br></div>I think this also runs counter to how a number of SDP algorith=
ms are traditional written, where seqan puts the Horizontal sequence first,=
 which IIRC is traditionally the query not the reference (e.g. Baker &amp; =
Giancarlo (2002), <a href=3D"http://www.sciencedirect.com/science/article/p=
ii/S0196677402912149">http://www.sciencedirect.com/science/article/pii/S019=
6677402912149</a>)<br>&quot;&quot;&quot;<div>=C2=A0 =C2=A0 assignSource(row=
(alignment, 0), sequenceH);<br>=C2=A0 =C2=A0 assignSource(row(alignment, 1)=
, sequenceV);<br><br>=C2=A0 =C2=A0 Score&lt;int, Simple&gt; scoringScheme(2=
, -1, -2);<br><br>=C2=A0 =C2=A0 int result =3D bandedChainAlignment(alignme=
nt, seedChain, scoringScheme, 2);<br>&quot;&quot;&quot;</div><div><br></div=
><div>-Brett</div><img src=3D"http://t.sigopn03.com/e1t/o/5/f18dQhb0S7ks8dD=
MPbW2n0x6l2B9gXrN7sKj6v4fhjlVRzvbY8qSQGCVRzH2b1pctGFW4bXls31k1H6H0?si=3D473=
8980717789184&amp;pi=3Db5fd8ab2-96b9-4e3c-a160-2ff47456668e" style=3D"displ=
ay:none!important" height=3D"1" width=3D"1"></div>

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Subject: Re: [Seqan-dev] bandedChainAlignment default failing due to default k
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If you're asking for the seed chain used used generate the above example,
it's given in the above code:
"""
appendValue(seedChain, TSeed( 0,  0, 14));
appendValue(seedChain, TSeed(30, 31, 14));
"""

So the entire SeedChain is just equivalent to
"""
[ (0, 0, 14, 14),  (30, 31, 44, 45) ]
"""

Unless you mean something else by SeedChain?


Also I found another case of this in a larger sequence (over 100bp on each
side), such that I don't think it's a simple size-of-the-matrix issue:

Query:
TAACTCATCATCAGCAATCCGAACAAAACCGCTGAACCGACCCTCGGACAAACAACAACGGAGGAGGAGAGAGGA=
GAGAGGAGCAGTTCAGGCGGTTGATTACGGAGGATTAGAAATAC
Reference:
ACGCCATAGTGACTGGCGATGCTGTCGGAATGGACGATATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAG=
AGAGAGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGC

With a single matching 19mer seed in the dead center:
Query      50  AACAACAACGGAGGAGGAG  69
Reference  50  AACAACAACGGAGGAGGAG  69

What I except to see is something like this:
      0     .    :    .    :    .    :    .    :    .    :
        ------TAACTCAT-CATCAGCAAT-CCGAACAAAAC-C--GC-TGA-AC
              |   | || |  | | | | |||  |    | |  ||  || |
        GCTTGGT---T-ATGC--CGGTACTGCCGGGC----CTCTTGCGGGATAT

     50     .    :    .    :    .    :    .    :    .    :
        CGACCCTCGGACAAACAACAACGGAGGAGGA-GAGAGGAGAGAG-GA---
        |  | |||  || |||||||||||||||||| || | |||||||  |
        C-TCTCTC-AAC-AACAACAACGGAGGAGGAGGAAAAGAGAGAGATATCC

    100     .    :    .    :    .    :    .    :
        -GC-AGTTCAGG--CGGTTGATTACGGAGGATTAGA--AATAC
         || ||   |||  |||   | ||| | | | || |  ||
        CGCAAG---AGGCCCGG--CAGTACCG-GCA-TA-ACCAA---


Which I can then trim down to the core region I want here:
       0     .    :    .    :    .    :
        AACAACAACGGAGGAGGA-GAGAGGAGAGAG
        |||||||||||||||||| || | |||||||
        AACAACAACGGAGGAGGAGGAAAAGAGAGAG


But instead, if my bandExtension is below 14 I get this garbage instead:
      0     .    :    .    :    .    :    .    :    .    :
        -------------------------------------TAACTCATCATCA
                                             || ||| || |||
        GCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCTC-TC-TCA

     50     .    :    .    :    .    :    .    :    .    :
        GCAATCCGAACAAAACCGCTGAACCGACCCTCGGACAAACAACAACGGAG
         |||  | |||  || ||  | |  |      |||  || ||  |  ||
        ACAA--C-AAC--AA-CG--G-A--G----GAGGAGGAA-AA-GA--GA-

    100     .    :    .    :    .    :    .    :    .    :
        GAGGAGA----G-AGGAGAGAG---GAGCAGTTCAGGCGGTTGATTACGG
        || || |    | |  |||| |   | |||| | |  |||   || ||
        GA-GATATCCCGCA--AGAG-GCCCG-GCAG-T-A-CCGG--CATAACCA

    150     .    :
        AGGATTAGAAATAC
        |
        A-------------


-Brett

On Wed, Jun 3, 2015 at 8:28 AM, Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de>
wrote:

>  Hi Brett,
>
>  the k-Parameter specifies the band width around seeds given by the
> passed seed chain. This is compliant to the banded chain alignment
> algorithm described in the LAGAN paper.
> So instead of taking the seed as is, one can compute a banded DP around
> the seed to find the optimal trace into and out of the seed.
>
>  My best guess, in your example is, that the entire alignment matrix is
> to small for a band extension of 15.
> Nevertheless it should work, but maybe this is an uncovered border case.
> Can you please supply the seed chain?
> It shouldn=E2=80=99t be to much on these small sequences?
>
>  Cheers,
>
>  Ren=C3=A9
>
>   On 23 May 2015, at 00:53, Brett Bowman <bnbowman@gmail.com> wrote:
>
>  I'm trying to align two highly similar sequences found via Kmer search:
>  Query =3D "ATCTCTCTCAACAAAACAACGAGGAGGAGTGAAAAGAGAGAGAT"
> Reference =3D "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT"
>
>  The expected alignment looks like this:
>
>  Score: 80
>       0     .    :    .    :    .    :    .    :    .
>         ATCTCTCTCAACAA-AACAAC-GAGGAGGAGTGAAAAGAGAGAGAT
>         |||||||||||||| |||||| ||||||||| ||||||||||||||
>         ATCTCTCTCAACAACAACAACGGAGGAGGAG-GAAAAGAGAGAGAT
>
>  But when I align it using the default values suggested by the tutorial,
> it doesn't show any inserted gaps at all, and I wind up with this instead=
:
>
>  Score: 80
>       0     .    :    .    :    .    :    .    :
>           ATCTCTCTCAACAAAACAACGAGGAGGAGTGAAAAGAGAGAGAT
>         |||||||||||||| |  |   |  |  | | |||
>         ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGA
>
>  I finally traced it down to the k-value (bandExtension value) passed
> into the alignment algorithm - values of K <=3D 13 succeed and generate t=
he
> top-most alignment, while the values of 14-15 like the default (15) repor=
t
> the low-quality alignment.
>
>  Yet oddly, both alignments report the correct alignment score at the end
> - so it's not failing, precisely.  It's just not storing or displaying th=
e
> correct alignment.
>
>  So I have two questions:
> 1) What exactly does the  k / bandExtension variable do?
> 2) What is going on here?
>
>  My code is pasted below for your use.
>
>  Sincerely,
> -Brett
>
>  """
>       #include <seqan/seeds.h>
>
>       using namespace seqan;
>
>       DnaString query =3D "ATCTCTCTCAACAAAACAACGAGGAGGAGTGAAAAGAGAGAGAT";
>      DnaString ref   =3D "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT";
>
>      typedef Seed<Simple> TSeed;
>      String<TSeed> seedChain;
>      appendValue(seedChain, TSeed( 0,  0, 14));
>      appendValue(seedChain, TSeed(30, 31, 14));
>      Score<int, Simple> scoringScheme(2, -1, -2);
>
>      Align<DnaString, ArrayGaps> alignment1;
>      resize(rows(alignment1), 2);
>      assignSource(row(alignment1, 0), query);
>      assignSource(row(alignment1, 1), ref);
>
>      Align<DnaString, ArrayGaps> alignment2;
>      resize(rows(alignment2), 2);
>      assignSource(row(alignment2, 0), query);
>      assignSource(row(alignment2, 1), ref);
>
>      int result1 =3D bandedChainAlignment(alignment1, seedChain,
> scoringScheme, 14);
>      std::cout << "Score: " << result1 << std::endl;
>      std::cout << alignment1 << std::endl;
>
>      int result2 =3D bandedChainAlignment(alignment2, seedChain,
> scoringScheme, 13);
>      std::cout << "Score: " << result2 << std::endl;
>      std::cout << alignment2 << std::endl;
>  """
>  _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>
>  ---
>
>  Ren=C3=A9 Rahn
> Ph.D. Student
> --------------------------------
>  Tel:  (+49) 30 838 75137
> Mail: rene.rahn@fu-berlin.de
> --------------------------------
>  Institute of Computer Science
> Algorithmic Bioinformatics (ABI)
> --------------------------------
> Freie Universit=C3=A4t Berlin
> Takustra=C3=9Fe 9
> 14195 Berlin
> --------------------------------
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
>

--e89a8f83abb9a8ab67051805387d
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>If you&#39;re asking for the seed chain used used gen=
erate the above example, it&#39;s given in the above code:</div><div>&quot;=
&quot;&quot;</div><div><div style=3D"font-size:12.8000001907349px">appendVa=
lue(seedChain, TSeed( 0, =C2=A00, 14));</div><div style=3D"font-size:12.800=
0001907349px">appendValue(seedChain, TSeed(30, 31, 14));</div></div><div>&q=
uot;&quot;&quot;</div><div><br></div><div>So the entire SeedChain is just e=
quivalent to</div><div>&quot;&quot;&quot;</div><div>[ (0, 0, 14, 14), =C2=
=A0(30, 31, 44, 45) ]</div><div>&quot;&quot;&quot;</div><div><br></div><div=
>Unless you mean something else by SeedChain?</div><div><br></div><div><br>=
</div><div>Also I found another case of this in a larger sequence (over 100=
bp on each side), such that I don&#39;t think it&#39;s a simple size-of-the=
-matrix issue:</div><div><br></div><div>Query:=C2=A0<br></div><div><div><fo=
nt face=3D"monospace, monospace">TAACTCATCATCAGCAATCCGAACAAAACCGCTGAACCGACC=
CTCGGACAAACAACAACGGAGGAGGAGAGAGGAGAGAGGAGCAGTTCAGGCGGTTGATTACGGAGGATTAGAAAT=
AC<br></font></div><div>Reference:<br></div><div><font face=3D"monospace, m=
onospace">ACGCCATAGTGACTGGCGATGCTGTCGGAATGGACGATATCTCTCTCAACAACAACAACGGAGGA=
GGAGGAAAAGAGAGAGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGC</font></div><div><br=
></div><div>With a single matching 19mer seed in the dead center:</div><div=
><font face=3D"monospace, monospace">Query =C2=A0 =C2=A0 =C2=A050 =C2=A0AAC=
AACAACGGAGGAGGAG =C2=A069</font></div><div><div><font face=3D"monospace, mo=
nospace">Reference =C2=A050 =C2=A0AACAACAACGGAGGAGGAG =C2=A069</font></div>=
</div><div><br></div><div>What I except to see is something like this:</div=
><div><span style=3D"font-family:monospace,monospace">=C2=A0 =C2=A0 =C2=A0 =
0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=
=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=
=A0:=C2=A0</span><br></div><div><font face=3D"monospace, monospace">=C2=A0 =
=C2=A0 =C2=A0 =C2=A0 ------TAACTCAT-CATCAGCAAT-CCGAACAAAAC-C--GC-TGA-AC</fo=
nt></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 | =C2=A0 | || | =C2=A0| | | | ||| =C2=A0| =C2=A0 =
=C2=A0| | =C2=A0|| =C2=A0|| |=C2=A0</font></div><div><font face=3D"monospac=
e, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 GCTTGGT---T-ATGC--CGGTACTGCCGGGC-=
---CTCTTGCGGGATAT</font></div><div><font face=3D"monospace, monospace"><br>=
</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A05=
0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=
=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=
=A0:=C2=A0</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 CGACCCTCGGACAAACAACAACGGAGGAGGA-GAGAGGAGAGAG-GA---</font>=
</div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 =
| =C2=A0| ||| =C2=A0|| |||||||||||||||||| || | ||||||| =C2=A0| =C2=A0=C2=A0=
</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 C-TCTCTC-AAC-AACAACAACGGAGGAGGAGGAAAAGAGAGAGATATCC</font></div><div>=
<font face=3D"monospace, monospace"><br></font></div><div><font face=3D"mon=
ospace, monospace">=C2=A0 =C2=A0 100 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =
=C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =
=C2=A0: =C2=A0 =C2=A0</font></div><div><font face=3D"monospace, monospace">=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 -GC-AGTTCAGG--CGGTTGATTACGGAGGATTAGA--AATAC</fo=
nt></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0|| || =C2=A0 ||| =C2=A0||| =C2=A0 | ||| | | | || | =C2=A0|| =C2=
=A0=C2=A0</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 CGCAAG---AGGCCCGG--CAGTACCG-GCA-TA-ACCAA---</font></div><=
div><br></div><div><br></div><div>Which I can then trim down to the core re=
gion I want here:</div><div><span style=3D"font-family:monospace,monospace"=
>=C2=A0 =C2=A0 =C2=A0 =C2=A00 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0.=
 =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0</span><br></div><div><=
font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 AACAACAACGGA=
GGAGGA-GAGAGGAGAGAG</font></div><div><font face=3D"monospace, monospace">=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||||||| || | |||||||</font></div><di=
v><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 AACAACAAC=
GGAGGAGGAGGAAAAGAGAGAG</font></div><div><br></div><div><br></div><div>But i=
nstead, if my bandExtension is below 14 I get this garbage instead:</div><d=
iv><div><span style=3D"font-family:monospace,monospace">=C2=A0 =C2=A0 =C2=
=A0 0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =
=C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =
=C2=A0:=C2=A0</span><br></div><div><font face=3D"monospace, monospace">=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 -------------------------------------TAACTCATCATCA=
</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0|| ||| ||=
 |||</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 GCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCTC-TC-TCA</font></div><=
div><font face=3D"monospace, monospace"><br></font></div><div><font face=3D=
"monospace, monospace">=C2=A0 =C2=A0 =C2=A050 =C2=A0 =C2=A0 . =C2=A0 =C2=A0=
: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0=
. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0</font></div><div><font=
 face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 GCAATCCGAACAAAAC=
CGCTGAACCGACCCTCGGACAAACAACAACGGAG</font></div><div><font face=3D"monospace=
, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0||| =C2=A0| ||| =C2=A0|| || =
=C2=A0| | =C2=A0| =C2=A0 =C2=A0 =C2=A0||| =C2=A0|| || =C2=A0| =C2=A0||=C2=
=A0</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=
=A0 =C2=A0 ACAA--C-AAC--AA-CG--G-A--G----GAGGAGGAA-AA-GA--GA-</font></div><=
div><font face=3D"monospace, monospace"><br></font></div><div><font face=3D=
"monospace, monospace">=C2=A0 =C2=A0 100 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=
=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=
=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0</font></div><div><font face=
=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 GAGGAGA----G-AGGAGAGA=
G---GAGCAGTTCAGGCGGTTGATTACGG</font></div><div><font face=3D"monospace, mon=
ospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 || || | =C2=A0 =C2=A0| | =C2=A0|||| | =
=C2=A0 | |||| | | =C2=A0||| =C2=A0 || || =C2=A0</font></div><div><font face=
=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 GA-GATATCCCGCA--AGAG-=
GCCCG-GCAG-T-A-CCGG--CATAACCA</font></div><div><font face=3D"monospace, mon=
ospace"><br></font></div><div><font face=3D"monospace, monospace">=C2=A0 =
=C2=A0 150 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0=C2=A0</font></div><=
div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 AGGATTA=
GAAATAC</font></div><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =
=C2=A0 =C2=A0 | =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0</font></div=
><div><font face=3D"monospace, monospace">=C2=A0 =C2=A0 =C2=A0 =C2=A0 A----=
---------</font></div></div><div><br></div><div><br></div><div>-Brett</div>=
</div><img src=3D"http://t.sigopn03.com/e1t/o/5/f18dQhb0S7ks8dDMPbW2n0x6l2B=
9gXrN7sKj6v4fhjlVRzvbY8qSQGCVRzH2b1pctGFW4bXls31k1H6H0?si=3D473898071778918=
4&amp;pi=3D9d7d02ab-7f38-45ed-c675-dafdd083f763" style=3D"display:none!impo=
rtant" height=3D"1" width=3D"1"></div><div class=3D"gmail_extra"><br><div c=
lass=3D"gmail_quote">On Wed, Jun 3, 2015 at 8:28 AM, Rahn, Ren=C3=A9 <span =
dir=3D"ltr">&lt;<a href=3D"mailto:rene.maerker@fu-berlin.de" target=3D"_bla=
nk">rene.maerker@fu-berlin.de</a>&gt;</span> wrote:<br><blockquote class=3D=
"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding=
-left:1ex">



<div style=3D"word-wrap:break-word">
Hi Brett,=C2=A0
<div><br>
</div>
<div>the k-Parameter specifies the band width around seeds given by the pas=
sed seed chain. This is compliant to the banded chain alignment algorithm d=
escribed in the LAGAN paper.</div>
<div>So instead of taking the seed as is, one can compute a banded DP aroun=
d the seed to find the optimal trace into and out of the seed.</div>
<div><br>
</div>
<div>My best guess, in your example is, that the entire alignment matrix is=
 to small for a band extension of 15.=C2=A0</div>
<div>Nevertheless it should work, but maybe this is an uncovered border cas=
e. Can you please supply the seed chain?</div>
<div>It shouldn=E2=80=99t be to much on these small sequences?</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Ren=C3=A9</div>
<div><br>
</div>
<div>
<div>
<blockquote type=3D"cite"><div><div class=3D"h5">
<div>On 23 May 2015, at 00:53, Brett Bowman &lt;<a href=3D"mailto:bnbowman@=
gmail.com" target=3D"_blank">bnbowman@gmail.com</a>&gt; wrote:</div>
<br>
</div></div><div><div><div class=3D"h5">
<div dir=3D"ltr">I&#39;m trying to align two highly similar sequences found=
 via Kmer search:
<div>
<div>
<div>Query =3D &quot;ATCTCTCTCAACAAAACAACGAGGAGGAGTGAAAAGAGAGAGAT&quot;</di=
v>
<div>Reference =3D &quot;ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT&quot=
;<br>
</div>
</div>
<div><br>
</div>
<div>The expected alignment looks like this:</div>
<div>
<div><br>
</div>
<div>Score: 80</div>
<div>=C2=A0 =C2=A0 =C2=A0 0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =
=C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =
=C2=A0 =C2=A0. =C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 ATCTCTCTCAACAA-AACAAC-GAGGAGGAGTGAAAAGAGAG=
AGAT</div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||| |||||| ||||||||| ||||||||||=
||||</div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 ATCTCTCTCAACAACAACAACGGAGGAGGAG-GAAAAGAGAG=
AGAT</div>
</div>
<div><br>
</div>
<div>But when I align it using the default values suggested by the tutorial=
, it doesn&#39;t show any inserted gaps at all, and I wind up with this ins=
tead:<br>
</div>
<div><br>
</div>
<div>Score: 80</div>
<div>=C2=A0 =C2=A0 =C2=A0 0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =
=C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =
=C2=A0 =C2=A0=C2=A0<br>
</div>
</div>
<div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 ATCTCTCTCAACAAAACAACGAGGAGGAGTGAAAAGAGAGAG=
AT</div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||| | =C2=A0| =C2=A0 | =C2=A0| =
=C2=A0| | ||| =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0 =C2=A0 ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGA=
GA</div>
</div>
<div><br>
</div>
<div>I finally traced it down to the k-value (bandExtension value) passed i=
nto the alignment algorithm - values of K &lt;=3D 13 succeed and generate t=
he top-most alignment, while the values of 14-15 like the default (15) repo=
rt the low-quality alignment.
 =C2=A0</div>
<div><br>
</div>
<div>Yet oddly, both alignments report the correct alignment score at the e=
nd - so it&#39;s not failing, precisely.=C2=A0 It&#39;s just not storing or=
 displaying the correct alignment.</div>
<div><br>
</div>
<div>So I have two questions:</div>
<div>1) What exactly does the =C2=A0k / bandExtension variable do?</div>
<div>2) What is going on here?</div>
<div><br>
</div>
<div>My code is pasted below for your use.</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>-Brett</div>
<div><br>
</div>
<div>&quot;&quot;&quot;</div>
<div>
<div>=C2=A0 =C2=A0 =C2=A0#include &lt;seqan/seeds.h&gt;</div>
<div><br>
</div>
<div>=C2=A0 =C2=A0 =C2=A0using namespace seqan;</div>
<div><br>
</div>
<div>=C2=A0 =C2=A0 =C2=A0DnaString query =3D &quot;ATCTCTCTCAACAAAACAACGAGG=
AGGAGTGAAAAGAGAGAGAT&quot;;</div>
<div>=C2=A0 =C2=A0 =C2=A0DnaString ref =C2=A0 =3D &quot;ATCTCTCTCAACAACAACA=
ACGGAGGAGGAGGAAAAGAGAGAGAT&quot;;</div>
<div>=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0typedef Seed&lt;Simple&gt; TSeed;</div>
<div>=C2=A0 =C2=A0 =C2=A0String&lt;TSeed&gt; seedChain;</div>
<div>=C2=A0 =C2=A0 =C2=A0appendValue(seedChain, TSeed( 0, =C2=A00, 14));</d=
iv>
<div>=C2=A0 =C2=A0 =C2=A0appendValue(seedChain, TSeed(30, 31, 14));</div>
<div>=C2=A0 =C2=A0 =C2=A0Score&lt;int, Simple&gt; scoringScheme(2, -1, -2);=
</div>
<div>=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0Align&lt;DnaString, ArrayGaps&gt; alignment1;</div=
>
<div>=C2=A0 =C2=A0 =C2=A0resize(rows(alignment1), 2);</div>
<div>=C2=A0 =C2=A0 =C2=A0assignSource(row(alignment1, 0), query);</div>
<div>=C2=A0 =C2=A0 =C2=A0assignSource(row(alignment1, 1), ref);</div>
<div>=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0Align&lt;DnaString, ArrayGaps&gt; alignment2;</div=
>
<div>=C2=A0 =C2=A0 =C2=A0resize(rows(alignment2), 2);</div>
<div>=C2=A0 =C2=A0 =C2=A0assignSource(row(alignment2, 0), query);</div>
<div>=C2=A0 =C2=A0 =C2=A0assignSource(row(alignment2, 1), ref);</div>
<div>=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0int result1 =3D bandedChainAlignment(alignment1, s=
eedChain, scoringScheme, 14);</div>
<div>=C2=A0 =C2=A0 =C2=A0std::cout &lt;&lt; &quot;Score: &quot; &lt;&lt; re=
sult1 &lt;&lt; std::endl;</div>
<div>=C2=A0 =C2=A0 =C2=A0std::cout &lt;&lt; alignment1 &lt;&lt; std::endl;<=
/div>
<div>=C2=A0</div>
<div>=C2=A0 =C2=A0 =C2=A0int result2 =3D bandedChainAlignment(alignment2, s=
eedChain, scoringScheme, 13);</div>
<div>=C2=A0 =C2=A0 =C2=A0std::cout &lt;&lt; &quot;Score: &quot; &lt;&lt; re=
sult2 &lt;&lt; std::endl;</div>
<div>=C2=A0 =C2=A0 =C2=A0std::cout &lt;&lt; alignment2 &lt;&lt; std::endl;<=
/div>
</div>
<div>&quot;&quot;&quot;</div>
</div></div></div>
_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de" target=3D"_blank">seqan-dev=
@lists.fu-berlin.de</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
</div>
</blockquote>
</div>
<br>
<div>
<div style=3D"color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wra=
p:break-word">
<div><font face=3D"Courier New">---</font></div>
<div><font face=3D"Courier New"><br>
</font></div>
<div><font face=3D"Courier New">Ren=C3=A9 Rahn</font></div>
<div><font face=3D"Courier New">Ph.D. Student</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div>
<div><font face=3D"Courier New">Tel: =C2=A0<a href=3D"tel:%28%2B49%29%2030%=
20838%2075137" value=3D"+493083875137" target=3D"_blank">(+49) 30 838 75137=
</a></font></div>
<div><font face=3D"Courier New">Mail:=C2=A0<a href=3D"mailto:rene.rahn@fu-b=
erlin.de" target=3D"_blank">rene.rahn@fu-berlin.de</a></font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
<div><font face=3D"Courier New">Institute of Computer Science</font></div>
<div><font face=3D"Courier New">Algorithmic Bioinformatics (ABI)</font></di=
v>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
<div><font face=3D"Courier New">Freie Universit=C3=A4t Berlin</font></div>
<div><font face=3D"Courier New">Takustra=C3=9Fe 9</font></div>
<div><font face=3D"Courier New">14195 Berlin</font></div>
<div><font face=3D"Courier New">--------------------------------</font></di=
v>
</div>
</div>
<br>
</div>
</div>

<br>_______________________________________________<br>
seqan-dev mailing list<br>
<a href=3D"mailto:seqan-dev@lists.fu-berlin.de">seqan-dev@lists.fu-berlin.d=
e</a><br>
<a href=3D"https://lists.fu-berlin.de/listinfo/seqan-dev" target=3D"_blank"=
>https://lists.fu-berlin.de/listinfo/seqan-dev</a><br>
<br></blockquote></div><br></div>

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Date: Tue, 09 Jun 2015 11:32:24 +0200
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Hi everyone,
what do you think about adding Bountysource support to our github? Ther=
eby=20
people, companies or other groups could put bounties on feature request=
s or=20
bugs that are important to them, e.g. "add support for Format X - 500$"=
, "fix=20
build issue on powerpc - 20$" =E2=80=A6
Maybe this will motivate people to fix issues faster ;)
--=20
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be=
rlin

address     Institut f=C3=BCr Informatik
            Takustra=C3=9Fe 9
            Room 019
            14195 Berlin
telephone   +49 (0)30 838-75241
fax         +49 (0)30 838-75218
e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]



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haha, i like that. if i can fix it. lol.

2015-06-09 16:32 GMT+07:00 Hannes Hauswedell <hannes.hauswedell@fu-berlin.d=
e
>:

> Hi everyone,
> what do you think about adding Bountysource support to our github? Thereb=
y
> people, companies or other groups could put bounties on feature requests =
or
> bugs that are important to them, e.g. "add support for Format X - 500$",
> "fix
> build issue on powerpc - 20$" =E2=80=A6
> Maybe this will motivate people to fix issues faster ;)
> --
> Hannes Hauswedell
>
> PhD student
> Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berl=
in
>
> address     Institut f=C3=BCr Informatik
>             Takustra=C3=9Fe 9
>             Room 019
>             14195 Berlin
> telephone   +49 (0)30 838-75241
> fax         +49 (0)30 838-75218
> e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>

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<div dir=3D"ltr">haha, i like that. if i can fix it. lol.</div><div class=
=3D"gmail_extra"><br><div class=3D"gmail_quote">2015-06-09 16:32 GMT+07:00 =
Hannes Hauswedell <span dir=3D"ltr">&lt;<a href=3D"mailto:hannes.hauswedell=
@fu-berlin.de" target=3D"_blank">hannes.hauswedell@fu-berlin.de</a>&gt;</sp=
an>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border=
-left:1px #ccc solid;padding-left:1ex">Hi everyone,<br>
what do you think about adding Bountysource support to our github? Thereby<=
br>
people, companies or other groups could put bounties on feature requests or=
<br>
bugs that are important to them, e.g. &quot;add support for Format X - 500$=
&quot;, &quot;fix<br>
build issue on powerpc - 20$&quot; =E2=80=A6<br>
Maybe this will motivate people to fix issues faster ;)<br>
--<br>
Hannes Hauswedell<br>
<br>
PhD student<br>
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berlin=
<br>
<br>
address=C2=A0 =C2=A0 =C2=A0Institut f=C3=BCr Informatik<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Takustra=C3=9Fe 9<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Room 019<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 14195 Berlin<br>
telephone=C2=A0 =C2=A0+49 (0)30 838-75241<br>
fax=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0+49 (0)30 838-75218<br>
e-mail=C2=A0 =C2=A0 =C2=A0 hannes.hauswedell@[<a href=3D"http://molgen.mpg.=
de" target=3D"_blank">molgen.mpg.de</a>|<a href=3D"http://fu-berlin.de" tar=
get=3D"_blank">fu-berlin.de</a>]<br>
<br>
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--047d7b5d848d7134dc0518540056
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Has anyone seen this before?

"""
In file included from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
.h:83:0,
                 from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/include/pbsparse/FindSeedsConfig.h:43,
                 from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/polylabel/src/../include/postprimary/polylabel/labeler/control/Cont=
rolFilter.h:44,
                 from
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/polylabel/src/ControlFilter.cpp:45:
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment_traceback.h:
In instantiation of =E2=80=98void seqan::_glueTracebacks(TTraceSet&, TTrace=
Set&)
[with TTraceSet =3D seqan::StringSet<seqan::String<seqan::TraceSegment_<lon=
g
unsigned int, long unsigned int>, seqan::Alloc<> >, seqan::Owner<> >]=E2=80=
=99:
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment_impl.h:1246:58:
  required from =E2=80=98TScoreValue seqan::_computeAlignment(TTraceSet&, c=
onst
TSeedSet&, const TSequenceH&, const TSequenceV&, const
seqan::Score<TScoreValue, TScoreSpec>&, const seqan::Score<TScoreValue,
TScoreSpecGap>&, unsigned int, const
seqan::DPProfile_<seqan::BandedChainAlignment_<TFreeEndGaps,
TDPMatrixLocation>, TGapSpec, seqan::TracebackOn<TTracebackConfig> >&)
[with TTraceSet =3D seqan::StringSet<seqan::String<seqan::TraceSegment_<lon=
g
unsigned int, long unsigned int>, seqan::Alloc<> >, seqan::Owner<> >;
TSeedSet =3D seqan::String<seqan::Seed<seqan::Tag<seqan::Simple_> > >;
TSequenceH =3D seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>,
seqan::Alloc<> >; TSequenceV =3D seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna_>, seqan::Alloc<> >; TScoreValue =3D long int;
TScoreSpecAnchor =3D const seqan::Tag<seqan::BiAffine_>; TScoreSpecGap =3D
const seqan::Tag<seqan::BiAffine_>; TFreeEndGaps =3D
seqan::FreeEndGaps_<seqan::True, seqan::True, seqan::True, seqan::True>;
TDPMatrixLocation =3D seqan::Tag<seqan::BandedChainInnerDPMatrix_>; TGapSpe=
c
=3D seqan::Tag<seqan::AffineGaps_>; TTracebackConfig =3D
seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>,
seqan::Tag<seqan::GapsLeft_> >]=E2=80=99
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment_profile.h:255:47:
  required from =E2=80=98TScoreValue
seqan::_setupAndRunBandedChainAlignment(seqan::StringSet<seqan::String<TStr=
ing>,
TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&,
const seqan::Score<TScoreValue2, TScoreSpec>&, const
seqan::Score<TScoreValue, TScoreSpecGap>&, const
seqan::AlignConfig<TFirstRow, TFirstColumn, TLastColumn, TLastRow,
TACSpec>&, unsigned int, const TGapsPlacement&) [with TTraceSegment =3D
seqan::TraceSegment_<long unsigned int, long unsigned int>; TStringSetSpec
=3D seqan::Owner<>; TSeeds =3D
seqan::String<seqan::Seed<seqan::Tag<seqan::Simple_> > >; TSequenceH =3D
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<>
>; TSequenceV =3D seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna_>, seqan::Alloc<> >; TScoreValue =3D long int; TScoreSpecAnchor =
=3D
const seqan::Tag<seqan::BiAffine_>; TScoreSpecGap =3D const
seqan::Tag<seqan::BiAffine_>; bool TFirstRow =3D true; bool TFirstColumn =
=3D
true; bool TLastColumn =3D true; bool TLastRow =3D true; TACSpec =3D
seqan::Tag<seqan::Default_>; TGapsPlacement =3D seqan::Tag<seqan::GapsLeft_=
>]=E2=80=99
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment.h:202:115:
  required from =E2=80=98TScoreValue
seqan::bandedChainAlignment(seqan::Align<TSource, TSpec>&, const TSeeds&,
const seqan::Score<TScoreValue, TScoreSpec>&, const
seqan::Score<TScoreValue, TScoreSpecGap>&, const seqan::AlignConfig<TOP,
LEFT, RIGHT, BOTTOM, TACSpec>&, unsigned int) [with TSequence =3D
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<>
>; TAlignSpec =3D seqan::Tag<seqan::ArrayGaps_>; TSeeds =3D
seqan::String<seqan::Seed<seqan::Tag<seqan::Simple_> > >; TScoreValue =3D
long int; TScoreSpecAnchor =3D const seqan::Tag<seqan::BiAffine_>;
TScoreSpecGap =3D const seqan::Tag<seqan::BiAffine_>; bool TFirstRow =3D tr=
ue;
bool TFirstColumn =3D true; bool TLastColumn =3D true; bool TLastRow =3D tr=
ue;
TACSpec =3D seqan::Tag<seqan::Default_>]=E2=80=99
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment.h:221:101:
  required from =E2=80=98TScoreValue
seqan::bandedChainAlignment(seqan::Align<TSource, TSpec>&, const TSeeds&,
const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP,
LEFT, RIGHT, BOTTOM, TACSpec>&, unsigned int) [with TSequence =3D
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<>
>; TAlignSpec =3D seqan::Tag<seqan::ArrayGaps_>; TSeeds =3D
seqan::String<seqan::Seed<seqan::Tag<seqan::Simple_> > >; TScoreValue =3D
long int; TScoreSpec =3D const seqan::Tag<seqan::BiAffine_>; bool TFirstRow=
 =3D
true; bool TFirstColumn =3D true; bool TLastColumn =3D true; bool TLastRow =
=3D
true; TACSpec =3D seqan::Tag<seqan::Default_>]=E2=80=99
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/include/pbsparse/BandedAligner.h:190:49:
  required from here
/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/Post=
Primary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds=
/banded_chain_alignment_traceback.h:126:10:
warning: variable =E2=80=98isGlued=E2=80=99 set but not used [-Wunused-but-=
set-variable]
     bool isGlued =3D false;
"""

--Brett

--047d7b5d848d7134dc0518540056
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<div dir=3D"ltr"><div>Has anyone seen this before?</div><div><br></div>&quo=
t;&quot;&quot;<div><div>In file included from /home/UNIXHOME/bbowman/p4/sof=
tware/smrtanalysis/bioinformatics/staging/PostPrimary/sparsealignment/third=
-party/seqan-library-2.0.0/include/seqan/seeds.h:83:0,</div><div>=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0from /home/UNIXHOME/bbo=
wman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/sparsealig=
nment/include/pbsparse/FindSeedsConfig.h:43,</div><div>=C2=A0 =C2=A0 =C2=A0=
 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0from /home/UNIXHOME/bbowman/p4/so=
ftware/smrtanalysis/bioinformatics/staging/PostPrimary/polylabel/src/../inc=
lude/postprimary/polylabel/labeler/control/ControlFilter.h:44,</div><div>=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0from /home/UN=
IXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/=
polylabel/src/ControlFilter.cpp:45:</div><div>/home/UNIXHOME/bbowman/p4/sof=
tware/smrtanalysis/bioinformatics/staging/PostPrimary/sparsealignment/third=
-party/seqan-library-2.0.0/include/seqan/seeds/banded_chain_alignment_trace=
back.h: In instantiation of =E2=80=98void seqan::_glueTracebacks(TTraceSet&=
amp;, TTraceSet&amp;) [with TTraceSet =3D seqan::StringSet&lt;seqan::String=
&lt;seqan::TraceSegment_&lt;long unsigned int, long unsigned int&gt;, seqan=
::Alloc&lt;&gt; &gt;, seqan::Owner&lt;&gt; &gt;]=E2=80=99:</div><div>/home/=
UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimar=
y/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds/bande=
d_chain_alignment_impl.h:1246:58: =C2=A0 required from =E2=80=98TScoreValue=
 seqan::_computeAlignment(TTraceSet&amp;, const TSeedSet&amp;, const TSeque=
nceH&amp;, const TSequenceV&amp;, const seqan::Score&lt;TScoreValue, TScore=
Spec&gt;&amp;, const seqan::Score&lt;TScoreValue, TScoreSpecGap&gt;&amp;, u=
nsigned int, const seqan::DPProfile_&lt;seqan::BandedChainAlignment_&lt;TFr=
eeEndGaps, TDPMatrixLocation&gt;, TGapSpec, seqan::TracebackOn&lt;TTracebac=
kConfig&gt; &gt;&amp;) [with TTraceSet =3D seqan::StringSet&lt;seqan::Strin=
g&lt;seqan::TraceSegment_&lt;long unsigned int, long unsigned int&gt;, seqa=
n::Alloc&lt;&gt; &gt;, seqan::Owner&lt;&gt; &gt;; TSeedSet =3D seqan::Strin=
g&lt;seqan::Seed&lt;seqan::Tag&lt;seqan::Simple_&gt; &gt; &gt;; TSequenceH =
=3D seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan::Dna_&gt;, s=
eqan::Alloc&lt;&gt; &gt;; TSequenceV =3D seqan::String&lt;seqan::SimpleType=
&lt;unsigned char, seqan::Dna_&gt;, seqan::Alloc&lt;&gt; &gt;; TScoreValue =
=3D long int; TScoreSpecAnchor =3D const seqan::Tag&lt;seqan::BiAffine_&gt;=
; TScoreSpecGap =3D const seqan::Tag&lt;seqan::BiAffine_&gt;; TFreeEndGaps =
=3D seqan::FreeEndGaps_&lt;seqan::True, seqan::True, seqan::True, seqan::Tr=
ue&gt;; TDPMatrixLocation =3D seqan::Tag&lt;seqan::BandedChainInnerDPMatrix=
_&gt;; TGapSpec =3D seqan::Tag&lt;seqan::AffineGaps_&gt;; TTracebackConfig =
=3D seqan::TracebackConfig_&lt;seqan::Tag&lt;seqan::CompleteTrace_&gt;, seq=
an::Tag&lt;seqan::GapsLeft_&gt; &gt;]=E2=80=99</div><div>/home/UNIXHOME/bbo=
wman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/sparsealig=
nment/third-party/seqan-library-2.0.0/include/seqan/seeds/banded_chain_alig=
nment_profile.h:255:47: =C2=A0 required from =E2=80=98TScoreValue seqan::_s=
etupAndRunBandedChainAlignment(seqan::StringSet&lt;seqan::String&lt;TString=
&gt;, TStringSetSpec&gt;&amp;, const TSeeds&amp;, const TSequenceH&amp;, co=
nst TSequenceV&amp;, const seqan::Score&lt;TScoreValue2, TScoreSpec&gt;&amp=
;, const seqan::Score&lt;TScoreValue, TScoreSpecGap&gt;&amp;, const seqan::=
AlignConfig&lt;TFirstRow, TFirstColumn, TLastColumn, TLastRow, TACSpec&gt;&=
amp;, unsigned int, const TGapsPlacement&amp;) [with TTraceSegment =3D seqa=
n::TraceSegment_&lt;long unsigned int, long unsigned int&gt;; TStringSetSpe=
c =3D seqan::Owner&lt;&gt;; TSeeds =3D seqan::String&lt;seqan::Seed&lt;seqa=
n::Tag&lt;seqan::Simple_&gt; &gt; &gt;; TSequenceH =3D seqan::String&lt;seq=
an::SimpleType&lt;unsigned char, seqan::Dna_&gt;, seqan::Alloc&lt;&gt; &gt;=
; TSequenceV =3D seqan::String&lt;seqan::SimpleType&lt;unsigned char, seqan=
::Dna_&gt;, seqan::Alloc&lt;&gt; &gt;; TScoreValue =3D long int; TScoreSpec=
Anchor =3D const seqan::Tag&lt;seqan::BiAffine_&gt;; TScoreSpecGap =3D cons=
t seqan::Tag&lt;seqan::BiAffine_&gt;; bool TFirstRow =3D true; bool TFirstC=
olumn =3D true; bool TLastColumn =3D true; bool TLastRow =3D true; TACSpec =
=3D seqan::Tag&lt;seqan::Default_&gt;; TGapsPlacement =3D seqan::Tag&lt;seq=
an::GapsLeft_&gt;]=E2=80=99</div><div>/home/UNIXHOME/bbowman/p4/software/sm=
rtanalysis/bioinformatics/staging/PostPrimary/sparsealignment/third-party/s=
eqan-library-2.0.0/include/seqan/seeds/banded_chain_alignment.h:202:115: =
=C2=A0 required from =E2=80=98TScoreValue seqan::bandedChainAlignment(seqan=
::Align&lt;TSource, TSpec&gt;&amp;, const TSeeds&amp;, const seqan::Score&l=
t;TScoreValue, TScoreSpec&gt;&amp;, const seqan::Score&lt;TScoreValue, TSco=
reSpecGap&gt;&amp;, const seqan::AlignConfig&lt;TOP, LEFT, RIGHT, BOTTOM, T=
ACSpec&gt;&amp;, unsigned int) [with TSequence =3D seqan::String&lt;seqan::=
SimpleType&lt;unsigned char, seqan::Dna_&gt;, seqan::Alloc&lt;&gt; &gt;; TA=
lignSpec =3D seqan::Tag&lt;seqan::ArrayGaps_&gt;; TSeeds =3D seqan::String&=
lt;seqan::Seed&lt;seqan::Tag&lt;seqan::Simple_&gt; &gt; &gt;; TScoreValue =
=3D long int; TScoreSpecAnchor =3D const seqan::Tag&lt;seqan::BiAffine_&gt;=
; TScoreSpecGap =3D const seqan::Tag&lt;seqan::BiAffine_&gt;; bool TFirstRo=
w =3D true; bool TFirstColumn =3D true; bool TLastColumn =3D true; bool TLa=
stRow =3D true; TACSpec =3D seqan::Tag&lt;seqan::Default_&gt;]=E2=80=99</di=
v><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/stagi=
ng/PostPrimary/sparsealignment/third-party/seqan-library-2.0.0/include/seqa=
n/seeds/banded_chain_alignment.h:221:101: =C2=A0 required from =E2=80=98TSc=
oreValue seqan::bandedChainAlignment(seqan::Align&lt;TSource, TSpec&gt;&amp=
;, const TSeeds&amp;, const seqan::Score&lt;TScoreValue, TScoreSpec&gt;&amp=
;, const seqan::AlignConfig&lt;TOP, LEFT, RIGHT, BOTTOM, TACSpec&gt;&amp;, =
unsigned int) [with TSequence =3D seqan::String&lt;seqan::SimpleType&lt;uns=
igned char, seqan::Dna_&gt;, seqan::Alloc&lt;&gt; &gt;; TAlignSpec =3D seqa=
n::Tag&lt;seqan::ArrayGaps_&gt;; TSeeds =3D seqan::String&lt;seqan::Seed&lt=
;seqan::Tag&lt;seqan::Simple_&gt; &gt; &gt;; TScoreValue =3D long int; TSco=
reSpec =3D const seqan::Tag&lt;seqan::BiAffine_&gt;; bool TFirstRow =3D tru=
e; bool TFirstColumn =3D true; bool TLastColumn =3D true; bool TLastRow =3D=
 true; TACSpec =3D seqan::Tag&lt;seqan::Default_&gt;]=E2=80=99</div><div>/h=
ome/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPr=
imary/sparsealignment/include/pbsparse/BandedAligner.h:190:49: =C2=A0 requi=
red from here</div><div>/home/UNIXHOME/bbowman/p4/software/smrtanalysis/bio=
informatics/staging/PostPrimary/sparsealignment/third-party/seqan-library-2=
.0.0/include/seqan/seeds/banded_chain_alignment_traceback.h:126:10: warning=
: variable =E2=80=98isGlued=E2=80=99 set but not used [-Wunused-but-set-var=
iable]</div><div>=C2=A0 =C2=A0 =C2=A0bool isGlued =3D false;</div></div><di=
v>&quot;&quot;&quot;</div><div><br></div><div>--Brett</div><img src=3D"http=
://t.signauxdeux.com/e1t/o/5/f18dQhb0S1Ll8dDMPbW2n0x6l2B9gXrW7sKj5C56dQtgf3=
ZlND602?si=3D4738980717789184&amp;pi=3D3da35cc7-a344-4e84-e008-c49b7cb6b3e3=
" style=3D"display:none!important" height=3D"1" width=3D"1"></div>

--047d7b5d848d7134dc0518540056--



From hannes.hauswedell@fu-berlin.de Fri Jun 12 19:56:55 2015
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Subject: Re: [Seqan-dev] Strange Warning Message with SeqAn 2.0 / gcc 4.8
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On 12.06.2015 17:45, Brett Bowman wrote:
> Has anyone seen this before?

> /home/UNIXHOME/bbowman/p4/software/smrtanalysis/bioinformatics/staging/PostPrimary/sparsealignment/third-party/seqan-library-2.0.0/include/seqan/seeds/banded_chain_alignment_traceback.h:126:10:
> warning: variable ‘isGlued’ set but not used [-Wunused-but-set-variable]
>      bool isGlued = false;

Fixed by
https://github.com/h-2/seqan/commit/2466e0875e1127d1d0abf64cc8001ef2efbb6f6a

Best regards,
Hannes



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Thread-Topic: [Seqan-dev] bandedChainAlignment default failing due to default	k
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From: Yue Gan <gany.fml@gmail.com>
Date: Tue, 23 Jun 2015 17:07:32 -0500
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Subject: [Seqan-dev] SA interval from indices
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Hi,

After created indices (I am using indexEsa), how do you search pattern by
using them?

I only know you can create a finder based on the indices, and search
pattern using finder based on the tutorial. But finder sometimes does not
seems very convenient to me. Sometime I only need the occ value of the
pattern, not their position, so I have to do:

    int num_cout;
    while (find(Finder, "TATAA"))
    {
        ++num_cout;
    }

And I do not think this is the right way to do it.... Is there any other
way that I can get the SAInterval directly?

Thanks!

Yue Gan

--047d7b33d42c1528910519369f5d
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<div dir=3D"ltr">Hi,<div><br></div><div>After created indices (I am using i=
ndexEsa), how do you search pattern by using them?=C2=A0</div><div><br></di=
v><div>I only know you can create a finder based on the indices, and search=
 pattern using finder based on the tutorial. But finder sometimes does not =
seems very convenient to me. Sometime I only need the occ value of the patt=
ern, not their position, so I have to do:</div><div><br></div><div><div>=C2=
=A0 =C2=A0 int num_cout;</div><div>=C2=A0 =C2=A0 while (find(Finder, &quot;=
TATAA&quot;))</div><div>=C2=A0 =C2=A0 {</div><div>=C2=A0 =C2=A0 =C2=A0 =C2=
=A0 ++num_cout;</div><div>=C2=A0 =C2=A0 }</div></div><div><br></div><div>An=
d I do not think this is the right way to do it.... Is there any other way =
that I can get the SAInterval directly?</div><div><br></div><div>Thanks!</d=
iv><div><br></div><div>Yue Gan</div></div>

--047d7b33d42c1528910519369f5d--



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From: =?utf-8?Q?C=C3=A9cile?= Moulin <cecile.moulin@u-psud.fr>
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Hi=20

I want to use SeqAn in a project so I read the guide (almost from getting s=
tated to Intergration with your own Build System). But when I try to compil=
e the example from Integration with your own Build System, a huge message a=
ppears... I found "error: no match for =E2=80=98operator=3D=E2=80=99 in =E2=
=80=98target =3D source=E2=80=99" and it ends with "make[1]: *** [main.o] E=
rreur 1" and "quit the directory..."=20

Does it come from me ? What can I do to solve it ?=20

Thanks a lot !=20

C=C3=A9cile=20

PS Sorry for my poor English=20

=09C=C3=A9cile MOULIN=20
M1 Bioinformatique et Biostatistiques (BIBS)=20

Bureau - non pr=C3=A9cis=C3=A9=20


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<html><body><div style=3D"font-family: times new roman, new york, times, se=
rif; font-size: 12pt; color: #000000"><div>Hi<br></div><div><br></div><div>=
I want to use SeqAn in a project so I read the guide (almost from getting s=
tated to Intergration with your own Build System). But when I try to compil=
e the example from Integration with your own Build System, a huge message a=
ppears... I found "error: no match for =E2=80=98operator=3D=E2=80=99 in =E2=
=80=98target =3D source=E2=80=99" and it ends with "make[1]: *** [main.o] E=
rreur 1" and "quit the directory..."<br><br></div><div>Does it come from me=
 ? What can I do to solve it ? <br></div><div><br></div><div>Thanks a lot !=
<br></div><div><br></div><div>C=C3=A9cile<br></div><div><br></div><div>PS S=
orry for my poor English<br></div><div><br></div><div><span name=3D"x"></sp=
an>&nbsp;<table class=3D"mceItemTable" xmlns=3D"urn:zimbraAccount"><tbody><=
tr><td><img alt=3D"Universit=C3=A9 Paris-Sud" src=3D"https://zimbra.u-psud.=
fr/public/z_logo_signature.png" style=3D"border: 0pt none;width:120px;heigh=
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height: 107px; background: url(data:image/png;"></td><td valign=3D"top"><sp=
an style=3D"font-size: 10pt" data-mce-style=3D"font-size: 10pt;"><b>C=C3=A9=
cile MOULIN</b><br>M1 Bioinformatique et Biostatistiques (BIBS)<br><br>Bure=
au - non pr=C3=A9cis=C3=A9<br> </span></td></tr></tbody></table><span name=
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Sorry for the last mail, I found the solution here https://github.com/seqan=
/seqan/issues/926=20

Sorry again=20
=09C=C3=A9cile MOULIN=20
M1 Bioinformatique et Biostatistiques (BIBS)=20

Bureau - non pr=C3=A9cis=C3=A9=20



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<html><body><div style=3D"font-family: times new roman, new york, times, se=
rif; font-size: 12pt; color: #000000"><div>Sorry for the last mail, I found=
 the solution here <a href=3D"https://github.com/seqan/seqan/issues/926">ht=
tps://github.com/seqan/seqan/issues/926</a><br></div><div><br></div><div>So=
rry again<br></div><div style=3D"color:#000;font-weight:normal;font-style:n=
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rif; font-size: 12pt; color: #000000" data-mce-style=3D"font-family: times =
new roman, new york, times, serif; font-size: 12pt; color: #000000;"><div><=
span></span>&nbsp;<table class=3D"mceItemTable"><tbody><tr><td><img src=3D"=
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ORK5CYII=3D" src=3D"https://zimbra.u-psud.fr/public/z_logo_signature.png" d=
ata-mce-src=3D"https://zimbra.u-psud.fr/public/z_logo_signature.png" data-m=
ce-style=3D"border: 0pt none; width: 120px; height: 107px; background: url(=
data:image/png;"></td><td valign=3D"top"><span style=3D"font-size: 10pt" da=
ta-mce-style=3D"font-size: 10pt;"><span style=3D"font-size: 10pt" data-mce-=
style=3D"font-size: 10pt;"><b>C=C3=A9cile MOULIN</b><br>M1 Bioinformatique =
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nt-size: 10pt" data-mce-style=3D"font-size: 10pt;">Bureau - non pr=C3=A9cis=
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