From hannes.hauswedell@fu-berlin.de Fri Feb 02 22:40:37 2018 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1ehj4W-002j7x-CC>; Fri, 02 Feb 2018 22:40:36 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1ehj4W-003FwA-8X>; Fri, 02 Feb 2018 22:40:36 +0100 Received: from [46.183.103.8] (helo=arothron.my.domain) by inpost2.zedat.fu-berlin.de (Exim 4.85) with esmtpsa (TLSv1.2:DHE-RSA-AES128-SHA:128) (envelope-from ) id <1ehj4U-0007Ut-87>; Fri, 02 Feb 2018 22:40:36 +0100 To: seqan-dev@lists.fu-berlin.de From: Hannes Hauswedell Message-ID: <0cbf4643-cc99-ce09-bcbb-8faee9395325@fu-berlin.de> Date: Fri, 2 Feb 2018 22:40:31 +0100 User-Agent: Mozilla/5.0 (X11; OpenBSD amd64; rv:52.0) Gecko/20100101 Thunderbird/52.2.1 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Language: en-GB Content-Transfer-Encoding: 8bit X-Originating-IP: 46.183.103.8 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1517607636-000005A1-8C0BBA80/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, T_RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: seqan-team@lists.fu-berlin.de Subject: [Seqan-dev] Release of SeqAn 2.4 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 02 Feb 2018 21:40:37 -0000 We are pleased to announce the release of version 2.4 of the SeqAn library and updated versions of the official SeqAn-based applications. The alignment module has received significant updates and a parallised interface. Beyond simple multi-threading the alignment module can utilise the vector extensions of modern CPUs (SSE4, AVX2, AVX512) resulting in very impressive speed-ups, especially on long sequences. In fact speed-ups of ~2000x over the serial case have been measured (AVX512 and 40 threads VS no vectorisation and one thread). The details are due to be published soon. The indexing module now also offers a parallelised interface which distributes multiple searches over the available CPU cores. Furthermore “optimal search schemes” can now be used for performing even faster searches with multiple errors. A preprint documenting these algorithms is available here: https://arxiv.org/abs/1711.02035 The ReducedAminoAcid module now offers more reductions based on more recent research and VCF I/O is now compliant to version 4.2 of the specification, i.e. rows with only eight fields are accepted. Major work went into fixing SeqAn platform support on non-canonical and big endian platforms, we are proud that also binary formats like BAM pass all tests on platforms like PowerPC64 and ARM64. All main release architectures of Debian GNU/Linux are now well supported and automatically tested. Sparc64 is one of the few platforms known not to work. We have improved compatibility with new compilers and the C++17 standard so SeqAn should generate no warnings in 2018, even with stricter warning levels. Finally we would like to announce that this is going to be the last feature release of SeqAn2. Most of our effort is going into the development of SeqAn3, now, another announcement will cover this shortly. Patch-level releases of SeqAn2 may, however, be released if we find serious bugs or regressions. *Further links* Full Changelog: https://github.com/seqan/seqan/blob/master/CHANGELOG.rst Downloads (also applications): http://packages.seqan.de Homepage: http://www.seqan.de -- Hannes Hauswedell PhD candidate Max Planck Institute for Molecular Genetics / Freie Universität Berlin address Institut für Informatik Takustraße 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] From august.guang@gmail.com Thu Feb 22 17:06:02 2018 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1eotNi-003fe9-9D>; Thu, 22 Feb 2018 17:06:02 +0100 Received: from mail-oi0-f47.google.com ([209.85.218.47]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1eotNi-002wFx-0f>; Thu, 22 Feb 2018 17:06:02 +0100 Received: by mail-oi0-f47.google.com with SMTP id u6so4047041oiv.9 for ; Thu, 22 Feb 2018 08:06:00 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=1dDqLXJsN8xSWSTW4WfMaF69PhhfI5+LwGJAFg2ejKQ=; b=dv4bIxclC6TiG1a/R7Aw2UJbKQV4JJR+yMcz0oyrJWinFn+Z5MDOvWQtQUTlWK6sIO edYK47s5INHgV8utOLXPJGICrT3Oy3RasbupG708oNCiIZPUenxqrCtyDLlhyF8WcZEQ X8rxL6CxhU8tAiPHEVvLkWdb0Xi0JeKmbZ2H1JCFjxmzbV8Ahde+WW3JEL4cittowsCJ YvP0aBxKQV/DcKzg3TXtZmwlH6jyjhrLo7NpyKMO+Mki2u3Fs2Eflo8ZRoTtb8uPeiIV knTnbHncOMOY+SJ/Lx8+ZoExcRafm2wpnB6QN+anPuXEdJhMc15LvmWujyKAx9NjvCCM a0aw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=1dDqLXJsN8xSWSTW4WfMaF69PhhfI5+LwGJAFg2ejKQ=; b=aYZMuaE/mFZSn6U1+ZqH9z2z00Kr7s68qtIzfZCwIDq/jCVfgSzuR8eSMTMXf4I5Sh 4OLaKVpjt0j5pN/+flKN0PAjTlBoAgQ8hM/s1BY/EBMGraD7lmMAn3IG+v/BJdW8fwR3 181ZQZb2qQQ9IqQsZyLNsS2fc5CYaCLoJYqK0q86luwVWUYMmxod56LNYUVLtf/41SFZ W0Vp9BDCWhNZM+WHEODtq5vepJocbbNNYaJcSa/7lZAOLpSt+ydkqXIqduTA0m9f8p+x HigN43LWA6qJqDLOYC6wM+R0gFrN8rAZIV8aRyR2N9FT/yDvIWkoCRJ4rht99DpBJ3uW Lvgw== X-Gm-Message-State: APf1xPDhCNBOPfQB8zU3wzIHCsxyMrLe0XHXZuEtlg55dvRn6mOJXO8K pDQETlBpnkl5yM8oeyg2Y7mkupwhrqhK2wArab8WFoig X-Google-Smtp-Source: AH8x226UmvQHmMqs8uvnV869pZ7p6kZ+lOe49/loI/SPZ/LgNesLzOGLV2sJZSFHhh14dWOitdsPxUjnE2xeIT++u8g= X-Received: by 10.202.83.129 with SMTP id h123mr5015159oib.228.1519315558899; Thu, 22 Feb 2018 08:05:58 -0800 (PST) MIME-Version: 1.0 Received: by 10.157.17.147 with HTTP; Thu, 22 Feb 2018 08:05:38 -0800 (PST) From: August Guang Date: Thu, 22 Feb 2018 11:05:38 -0500 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="001a113db62c30ae1b0565cf38e1" X-Originating-IP: 209.85.218.47 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1519315562-000005A1-43F518C7/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.368344, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.1 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_NONE, RCVD_IN_MSPIKE_H2, SPF_PASS,URIBL_BLOCKED X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] placing seqan headers into R package X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 22 Feb 2018 16:06:02 -0000 --001a113db62c30ae1b0565cf38e1 Content-Type: text/plain; charset="UTF-8" Hi, I would like to package the SeqAn headers for easy use in a few R packages I will be writing with my team, the Computational Biology Core at Brown University in the US. Would this be ok with you all? I am leaving the license as BSD 3 clause as well, and if you would like to make any additions to the license please let me know. You can view the current state of the repository here: https://github.com/compbiocore/RSeqAn Thanks, august --001a113db62c30ae1b0565cf38e1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I would like to package the SeqAn h= eaders for easy use in a few R packages I will be writing with my team, the= Computational Biology Core at Brown University in the US. Would this be ok= with you all? I am leaving the license as BSD 3 clause as well, and if you= would like to make any additions to the license please let me know.
<= div>
You can view the current state of the repository here:= =C2=A0https://github.com/= compbiocore/RSeqAn

Thanks,
august
--001a113db62c30ae1b0565cf38e1-- From hannes.hauswedell@fu-berlin.de Mon Feb 26 13:49:18 2018 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1eqIDV-0016cy-I8>; Mon, 26 Feb 2018 13:49:17 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1eqIDV-002kpG-EV>; Mon, 26 Feb 2018 13:49:17 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1eqIDV-001pkl-8r>; Mon, 26 Feb 2018 13:49:17 +0100 From: Hannes Hauswedell To: August Guang Date: Mon, 26 Feb 2018 13:49:15 +0100 Message-ID: <6369393.BiE2NBDbOz@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1519649357-000005A1-D8541276/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, T_FILL_THIS_FORM_SHORT,T_RP_MATCHES_RCVD,URIBL_BLOCKED X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: SeqAn Development Subject: Re: [Seqan-dev] placing seqan headers into R package X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 26 Feb 2018 12:49:18 -0000 Am Donnerstag, 22. Februar 2018, 11:05:38 schrieb August Guang: > Hi, >=20 > I would like to package the SeqAn headers for easy use in a few R pac= kages > I will be writing with my team, the Computational Biology Core at Bro= wn > University in the US. Would this be ok with you all? I am leaving the= > license as BSD 3 clause as well, and if you would like to make any > additions to the license please let me know. >=20 > You can view the current state of the repository here: > https://github.com/compbiocore/RSeqAn >=20 > Thanks, > august Dear August, that's great to hear, feel very free to include it in your package. As = long as=20 the LICENSE file is shipped with the package there is no problem. Pleas= e also=20 include a link to www.seqan.de in your documentation and if possible al= so the=20 following note: "Please do not forget to cite SeqAn if you use this package in your ace= demic=20 work, even if only in auxiliary tools or pipelines: https://doi.org/10.1016/j.jbiotec.2017.07.017" That would be great! Thank you, Hannes --=20 Hannes Hauswedell Scientific staff & PhD candidate Freie Universit=C3=A4t Berlin / Max Planck Institute for Molecular Gene= tics 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