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From: Venitha Bernard <venithabernard@gmail.com>
Date: Wed, 6 Mar 2019 16:20:56 +0530
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Subject: [Seqan-dev] Mason2 Simulator Illumina Error Profile Input File format
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Hello.

I would like to know the format for creating an Illumina error profile file
to give as input to the Mason2 simulator.

Thank you!

Venitha

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<div dir="ltr"><div>Hello.</div><div><br></div><div>I would like to know the format for creating an Illumina error profile file to give as input to the Mason2 simulator.</div><div><br></div><div>Thank you!</div><div><br></div><div>Venitha<br></div></div>

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Subject: [Seqan-dev] Mason2: Could not open right/single-end output file
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Hello!

I am getting the error "Could not open right/single-end output file." when
I try to run Mason2. Please advise me on how to solve this problem.

Regards,
Venitha
IBAB, Bengaluru,
India

$ mason_simulator -ir Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa -n
160000000 --illumina-read-length 100 --out aedes_AaegL5_r1.fq.gz
--out-right aedes_AaegL5_r2.fq.gz

MASON SIMULATOR
===============

____INITIALIZING______________________________________________________________

Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file aedes_AaegL5_r1.fq.gz ... OK
Opening output file aedes_AaegL5_r2.fq.gz
.../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED!
(Uncaught exception of type MasonIOException: Could not open
right/single-end output file.)

stack trace:
  0                      [0x4c401d]
  1                      [0x4c96a6]
  2                      [0x4c96f1]
  3                      [0x4d4c38]
  4                      [0x467abf]
  5                      [0x468312]
  6                      [0x400b42]
  7                      [0x53c62b]
  8                      [0x405f51]

Aborted (core dumped)

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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>A lot of Seqan applications use BSD style licenses. That is very good!</div>

<div>&nbsp;</div>

<div>Some of the apps use more restrictive licenses such as GPL and LGPL. That makes the modern&nbsp;web apps, which are delivered to the browsers, thus deemed to be distributed,&nbsp;almost impossible to comply with the licenses without disclosing your entire website.</div>

<div>&nbsp;</div>

<div>For example, STELLAR is interesting, but it uses LGPL. Would you please license it with BSD style licenses?</div>

<div>&nbsp;</div>

<div>Thanks.</div>

<div>&nbsp;</div>

<div>&nbsp;</div></div></body></html>



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[note that this is not legal advice]

Am Sonntag, 17. M=C3=A4rz 2019, 18:24:00 CET schrieb Seqan Fan:
> A lot of Seqan applications use BSD style licenses. That is very good!
> =20
> Some of the apps use more restrictive licenses such as GPL and LGPL. That
> makes the modern web apps, which are delivered to the browsers, thus deem=
ed
> to be distributed, almost impossible to comply with the licenses without
> disclosing your entire website.

I am not sure what you are referring to here. Distributing source code or=20
binaries VIA a website does not make your web site a derivative of the=20
application and thus does not influence your choice of license.

What are you referring to with "web app"? Are you compiling Stellar into=20
Javascript or another interpreted language? In that case, still, the LGPL o=
nly=20
covers changes made immediately to the Stellar's code or code derived from =
it,=20
not some framework you use around it.
I don't see how it is "impossible to comply with this", but as Knut Reinert=
=20
mentioned, we are evaluating whether we can change the license.

>=20
> For example, STELLAR is interesting, but it uses LGPL. Would you please
> license it with BSD style licenses?=20

Please not that the BSD license also requires you to give attribution in yo=
ur=20
copyright notices and possibly in the documentation. And also, please cite =
our=20
work in case you publish derived work in academic contexts.

Thanks,
=2D-=20
Hannes Hauswedell

Scientific staff & PhD candidate
=46reie Universit=C3=A4t Berlin / Max Planck Institute for Molecular Geneti=
cs

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@fu-berlin.de



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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Precisely, the Stellar will be compiled to Javascript. Therefore, the web app, the &quot;Combined Works&quot; in the LGPL terms, is covered by the LGPL.</div>

<div>&nbsp;</div>

<div>One of the key requirements of the LGPL is to convey the application code &quot;in a form suitable for...the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work.&quot;</div>

<div>&nbsp;</div>

<div>The &quot;Linked Version&quot; is the Stellar, which is compiled into Javascript. Suppose the Stellar Javascript source code is fully distributed to you&nbsp;and you change one line of that&nbsp;code. How can you possibly recombine the application with your modified version of the Stellar, without the application source code? Mind you the application (framework code + Stellar Javascript)&nbsp;resides on the web server and is delivered to your browser on the fly upon an HTTP request.</div>

<div>&nbsp;</div>

<div>The Seqan is great. It would be very helpful if all the Seqan apps use the same license as the Seqan.</div>

<div>&nbsp;</div>

<div>Thanks.</div>

<div>&nbsp;</div>

<div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div name="quoted-content"><br/>
What are you referring to with &quot;web app&quot;? Are you compiling Stellar into<br/>
Javascript or another interpreted language? In that case, still, the LGPL only<br/>
covers changes made immediately to the Stellar&#39;s code or code derived from it,<br/>
not some framework you use around it.<br/>
I don&#39;t see how it is &quot;impossible to comply with this&quot;, but as Knut Reinert<br/>
mentioned, we are evaluating whether we can change the license.<br/>
<br/>
--<br/>
Hannes Hauswedell<br/>
<br/>
Scientific staff &amp; PhD candidate<br/>
Freie Universit&auml;t Berlin / Max Planck Institute for Molecular Genetics<br/>
<br/>
&nbsp;</div>
</div>
</div></div></body></html>



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Subject: [Seqan-dev] INSEGT wrong output format?
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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>The output file format of the INSEGT seems to be wrong.</div>

<div>&nbsp;</div>

<div>Take a look at this:&nbsp;https://github.com/seqan/seqan/blob/master/apps/insegt/example/readOutput.gff</div>

<div>&nbsp;</div>

<div>The extention name of the file is gff, but it does not conform to the GFF schema.</div>

<div>&nbsp;</div>

<div>GFF is supposed to have 9 fields for each line, but readOutput.gff has something like this:</div>

<div>&nbsp;</div>

<div>test_mRNA_3 test_chromosome + ENSG00000146556-18;ENSG00000146556-6 ENSG00000146556</div>

<div>&nbsp;</div>

<div>&nbsp;</div></div></body></html>