From dr.diaafayed@gmail.com Thu Jan 16 19:42:26 2020 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:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1isA60-0015bK-3O>; Thu, 16 Jan 2020 19:42:20 +0100 Received: from mail-wr1-f65.google.com ([209.85.221.65]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (envelope-from ) id <1isA5z-004Anp-Vx>; Thu, 16 Jan 2020 19:42:20 +0100 Received: by mail-wr1-f65.google.com with SMTP id c14so20230502wrn.7 for ; Thu, 16 Jan 2020 10:42:18 -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=ggRZZqg7ow/ypMPF4zgBqMoN9Y1wyMu6RSn9yppVu0I=; b=GC5tZVD89q2SicVqsbEYNDX99Stv5ZwKAFLNu2oixDdu4gwCdskiWKt0zZgIDJVknv yrCpvps4AXtoZ78lKmgg+9W5t5a07tBc8nlgXw4AgKp5ASq0OFaFDidPregn3sjdvLm1 FiknL5kuCLXVr88TVnKkU3eT7UVZs0cIHmx6bpme+dUHzF8kJJ7opi8xCectC3kSNDV0 vpUeTey7epWHXsHvosVZ3Em0mFUcMLPOT7+Xi8MzGrJbQ9nJFhnv2owwGjgfBgSAKEZ/ tYCBAupJkX8aPP24I4r4X70AFTGbpajgQ8QEqMwld5NHLbqZB0c8Ufgi7jOO1IIWbG4q Sn6g== X-Google-DKIM-Signature: v=1; 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charset="UTF-8" X-Originating-IP: 209.85.221.65 X-ZEDAT-Hint: T X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1579200140-000D41B9-0A520843/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.638143, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=1.3 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_FROM,FU_BOGO_UNSURE, RCVD_IN_MSPIKE_H2,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.3 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: x Subject: [Seqan-dev] full runnin X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 16 Jan 2020 18:42:27 -0000 plz I need full running example using external string and files From enrico.seiler@fu-berlin.de Wed Jan 22 15:54:38 2020 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iuHOw-004BhB-9u>; Wed, 22 Jan 2020 15:54:38 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iuHOw-0023jY-6z>; Wed, 22 Jan 2020 15:54:38 +0100 Received: from camex32.campus.fu-berlin.de ([130.133.170.222]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES256-GCM-SHA384:256) (envelope-from ) id <1iuHOv-003GY4-S2>; Wed, 22 Jan 2020 15:54:38 +0100 Received: from CAMEX30.campus.fu-berlin.de (130.133.170.220) by camex32.campus.fu-berlin.de (130.133.170.222) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.1591.10; Wed, 22 Jan 2020 15:54:36 +0100 Received: from CAMEX30.campus.fu-berlin.de ([fe80::542f:914a:242f:84db]) by CAMEX30.campus.fu-berlin.de ([fe80::542f:914a:242f:84db%6]) with mapi id 15.01.1591.017; Wed, 22 Jan 2020 15:54:36 +0100 From: "Seiler, Enrico Frank" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: SeqAn Release 3.0.1 Thread-Index: AQHV0TH7Zrgie6srbEixstozhwpsig== Message-ID: References: <0a33b094aaa149b1b72041f2399141d2@fu-berlin.de> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_F1E719EDDA1E49FBBBEB67B0420FD7B7fuberlinde_" MIME-Version: 1.0 Date: Wed, 22 Jan 2020 15:54:36 +0100 X-Original-Date: Wed, 22 Jan 2020 14:54:36 +0000 X-Originating-IP: 130.133.170.222 X-Original-X-Originating-IP: [130.133.175.152] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1579704878-00099802-F4B67A53/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.475771, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.3 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn Release 3.0.1 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 22 Jan 2020 14:54:38 -0000 --_000_F1E719EDDA1E49FBBBEB67B0420FD7B7fuberlinde_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable We are excited to present a new update of our SeqAn library. This release h= as been in the making for roughly half a year now and we are proud to prese= nt some great new features and also a lot of improvements with respect to r= untime and usability. You can find a comprehensive list of the changes in o= ur changelog. * Get to know SeqAn3 with our tutorials. * Visit our API documentation. * See the porting guide for some help on porting from SeqAn2. Note that 3.1.0 will be the first API stable release and interfaces in this= release might still change. [tada] Notable new features * We added support for type erasing semialphabets that allows you to manage semia= lphabets with the same alphabet size in one container. This can have a big = effect on your compile-time, in case you don't drink as much [coffee] as w= e do. * We added parallel support for the alignment algorithm. You can now configur= e the number of threads you want to use for the alignment computation. * One to command them all: Our argument parser now supports subcommands, such= as git pull. A How-to will guide you through setting this up for your tool. * The performance of the I/O was improved to allow faster file reading. Furth= er, we added support for reading and writing the CIGAR string through align= ment files. * We added several new ranges and views. Most notably, the seqan3::views::kme= r_hash view, which transforms a sequence into a range of k-mer hashes effic= iently. Another view of great practice is the seqan3::views::to, which can = be used to convert a view into a container. We also added aseqan3::dynamic_= bitset which is a dynamic version of the std::bitset. * Memory consumption of the (bidirectional) FM-Index for text collections was= reduced by 10%. [:trollface:] Notable API changes As much as we'd like to reduce inconsistencies between releases, we are som= etimes forced to change an interface either to improve usability or to foll= ow changes made by the ISO C++ committee. * All our concepts are named in the snake_case style (e.g. seqan3::Writ= ableAlphabet -> seqan3::writable_alphabet)! * The directory seqan3/range/view has been renamed to seqan3/range/view= s. * The namespace seqan3::view has been renamed to seqan3::views. * The CMake variable SEQAN3_VERSION_STRING defined by find_package(SEQA= N3) was renamed to SEQAN3_VERSION. You can find a comprehensive list of the changes in our changelog. [bug] Notable bug fixes * Copying and moving the seqan3::fm_index and seqan3::bi_fm_index now w= ork properly. * The translation table for nucleotide to amino acid translation was co= rrected. * The amino acid score matrices were corrected. [electric_plug] External dependencies * We now support ranges-v3 versions >=3D 0.10.0 and < 0.11.0, increasin= g the previous requirement of >=3D 0.5.0 and < 0.6.0. * We now support cereal version 1.3.0, increasing the previous requirem= ent of 1.2.2 --_000_F1E719EDDA1E49FBBBEB67B0420FD7B7fuberlinde_ Content-Type: text/html; charset="us-ascii" Content-ID: <83E956B89235754892F3FFF5D69D15AF@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable We are excited to present a new update of our SeqAn library. = This release has been in the making for roughly half a year now and we are = proud to present some great new features and also a lot of improvements with respect to runtime and usability. You = can find a comprehensive list of the changes in our changelog.
Note that 3.= 1.0 will be the first API stable release and interfaces in this release mig= ht still change.

3D"tada" Notable new features<= /h3>
  • We added sup= port for type erasing semialphabets that allows you to manage semialphabets with the same alphabet size in one cont= ainer. This can have a big effect on your compile-time, in case you don't d= rink as much 3D"coffee" as we do.
  • We added par= allel support for the alignment algorithm. You can now configure the number= of threads you want to use for the alignment computation.
  • One to comma= nd them all: Our argument parser now supports subcommands, such as git pull. A How-to will guide you through setting this up for your tool.
  • The performa= nce of the I/O was improved = to allow faster file reading. Further, we added support for reading and writing the CIGAR string through alignment files.<= /div>
  • We added sev= eral new ranges and views. Most notably, the seqan3::views::kmer_hash view, which transforms a sequence into a range of k-mer hashes efficiently. Another vi= ew of great practice is the seqan3::views::to, which can be used to convert = a view into a container. We also added aseqan3::dynamic_bi= tset which is a dynamic version of the std::bitset.
  • Memory consu= mption of the (bidirectional) FM-Index for text collections was reduced by = 10%.

3D":trollface= Notable API changes

As much as w= e'd like to reduce inconsistencies between releases, we are sometimes force= d to change an interface either to improve usability or to follow changes m= ade by the ISO C++ committee.
  • All our concepts are named in the snake_case style (e.g. seqan3::WritableAlphabet -> seqan3::writable_alphabet= )!
  • The directory&n= bsp;seqan3/range/view has been renamed to seqan3/range/views.
  • The namespace seqan3::view has been renamed to seqan3::views.
  • The CMake variable SEQAN3_VERSION_STR= ING defined by find_packag= e(SEQAN3) was renamed to SEQAN3_VERSION.
You can find= a comprehensive list of the changes in our changelog.

3D"bug" Notable bug fixes

  • Copying and moving the=  seqan3::fm_index and = ;seqan3::bi_fm_index now work properly.
  • The translation table for nucleotide to = amino acid translation was corrected.
  • The amino acid sco= re matrices were corrected.

3D"electric_plug" External dep= endencies

  • We now support ranges-v3 versions >=3D 0.10.0 and < 0.= 11.0, increasing the previous requirement of >=3D 0.5.0 and < 0.6.0.<= /li>
  • We now support cereal version 1.3.0, increasing the prev= ious requirement of 1.2.2

--_000_F1E719EDDA1E49FBBBEB67B0420FD7B7fuberlinde_-- From dr.diaafayed@gmail.com Wed Jan 22 19:10:40 2020 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:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iuKSa-000KJF-Q6>; Wed, 22 Jan 2020 19:10:36 +0100 Received: from mail-wr1-f52.google.com ([209.85.221.52]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (envelope-from ) id <1iuKSa-000TUQ-MW>; Wed, 22 Jan 2020 19:10:36 +0100 Received: by mail-wr1-f52.google.com with SMTP id d16so59487wre.10 for ; Wed, 22 Jan 2020 10:10:35 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to; bh=HmiVEt4r0tTjsbRTWRx534mIkIiV4MY/yXusMqEqtFQ=; b=YC4a4kH7c+eOJ4zT7RlJi7LnnWLRFQCFf4CUg6vrHZIEfVgdiveYLRsu9J9KsCW8sM yz1z6/RJDSVa4xRBZ1ITGRS5yC/UweQbcnFppdgws4BxJZc4+gm3/eq57nXcPiBQwSYS ozHSJGix+n2jnKckQ/t6iKvLZTWmNXFyu/iC1TorjZ9Zh9X12qyzDt5KAmX+buoL0JbX NJXC7P8kEOSVlrhMqpdWPnlJhkhtZpWZlKLcuREWrFBw9QK2pEO92IVPxKXcf6ieDjPC XBtZYA4YRG+CzAT3Q3aYc/dowEhXL9r2CSXM03zTNJOLltdfm2ytyFk9Gyz8ot+tVuD4 mm5Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to; bh=HmiVEt4r0tTjsbRTWRx534mIkIiV4MY/yXusMqEqtFQ=; b=mCF12bnPG2AqtIi2bwl+9OEsICY0tYGRYt1a2RoiNJsG7HH8pFgYCkSF15imILM05w SrSF/lPErwPU2k/SJaAd6hvhzRppl/yXRSz5dqPo/baA5o5Bksg2L3tjyRdEzO/Xq1MX 1k7CTtR5XFh81YLOzrE9BwxhN8x+KoT4cD7VZ3FZ/iYr3pv4lFmQM/1+Bs+Mo1h+mXv4 Io9SzZV3+1NsCS9TYUUABxIiCI5WIUcBaupKgPchLcxr5IPCCrsl+VCkK/WLbPE1/aUu V1bKEko7YfHAXns+lleULRWsMdV1NqoFtxGyI9Vx/4YBh7z8SyMmyYYiqZ3KcJ/GzJp6 qamw== X-Gm-Message-State: APjAAAXkPXp9ZUd0tY/c3xrz43qZyA+ipAMkS9mWf0olbM1+bgda/g6q zcBmybbNSlD8vSgcXFTIo9Wfzy1QaAsdMWooDcsaUg== X-Google-Smtp-Source: APXvYqyTsczbMJtQQRVm1Oz9Zx4W+evLrRB6TeBv6B3yOxpQkdZ05atT80qZzEWnqkdxYuDGPwUnZ6xNy4i7MXjEwkY= X-Received: by 2002:a5d:6390:: with SMTP id p16mr13144358wru.170.1579716634961; Wed, 22 Jan 2020 10:10:34 -0800 (PST) MIME-Version: 1.0 Received: by 2002:a05:600c:21a:0:0:0:0 with HTTP; Wed, 22 Jan 2020 10:10:34 -0800 (PST) In-Reply-To: References: <0a33b094aaa149b1b72041f2399141d2@fu-berlin.de> From: Diaa Fayed Date: Wed, 22 Jan 2020 20:10:34 +0200 Message-ID: To: SeqAn Development Content-Type: text/plain; charset="UTF-8" X-Originating-IP: 209.85.221.52 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1579716636-00099802-2900B2AF/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.489045, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_FROM,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.3 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn Release 3.0.1 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 22 Jan 2020 18:10:40 -0000 - I read about both SeqAn3 and SeqAn2. - Documentation and some algorithms have not implemented yet in SeqAn3 - SeqAn3 is based on very advanced C++ concepts I have not known about yet so I prefer to use SeqAn2.4 what is your opinion? ------------------------------------------------------------------------------------------------ On 1/22/20, Seiler, Enrico Frank wrote: > We are excited to present a new update of our SeqAn library. This release > has been in the making for roughly half a year now and we are proud to > present some great new features and also a lot of improvements with respect > to runtime and usability. You can find a comprehensive list of the changes > in our > changelog. > > * Get to know SeqAn3 with our > tutorials. > * Visit our API > documentation. > * See the porting > guide for some > help on porting from SeqAn2. > > Note that 3.1.0 will be the first API stable release and interfaces in this > release might still change. > [tada] Notable new features > > * > We added support for type erasing > semialphabets > that allows you to manage semialphabets with the same alphabet size in one > container. This can have a big effect on your compile-time, in case you > don't drink as much [coffee] as we do. > * > We added parallel support for the alignment algorithm. You can now configure > the number of threads you want to use for the alignment computation. > * > One to command them all: Our argument parser now supports subcommands, such > as git pull. A > How-to will > guide you through setting this up for your tool. > * > The performance of the I/O was improved to allow faster file reading. > Further, we added support for reading and writing the CIGAR string through > alignment files. > * > We added several new ranges and views. Most notably, the > seqan3::views::kmer_hash view, which transforms a sequence into a range of > k-mer hashes efficiently. Another view of great practice is the > seqan3::views::to, which can be used to convert a view into a container. We > also added aseqan3::dynamic_bitset which is a dynamic version of the > std::bitset. > * > Memory consumption of the (bidirectional) FM-Index for text collections was > reduced by 10%. > > [:trollface:] Notable API changes > As much as we'd like to reduce inconsistencies between releases, we are > sometimes forced to change an interface either to improve usability or to > follow changes made by the ISO C++ committee. > > * All our concepts are named in the snake_case style (e.g. > seqan3::WritableAlphabet -> seqan3::writable_alphabet)! > * The directory seqan3/range/view has been renamed to > seqan3/range/views. > * The namespace seqan3::view has been renamed to seqan3::views. > * The CMake variable SEQAN3_VERSION_STRING defined by > find_package(SEQAN3) was renamed to SEQAN3_VERSION. > > You can find a comprehensive list of the changes in our > changelog. > [bug] Notable bug fixes > > * Copying and moving the seqan3::fm_index and seqan3::bi_fm_index now > work properly. > * The translation table for nucleotide to amino acid translation was > corrected. > * The amino acid score matrices were corrected. > > [electric_plug] External dependencies > > * We now support ranges-v3 versions >= 0.10.0 and < 0.11.0, increasing > the previous requirement of >= 0.5.0 and < 0.6.0. > * We now support cereal version 1.3.0, increasing the previous > requirement of 1.2.2 > > From Rene.Rahn@fu-berlin.de Thu Jan 23 17:32:22 2020 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iufP3-002aEy-Dt>; Thu, 23 Jan 2020 17:32:21 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iufP3-002QZX-BN>; Thu, 23 Jan 2020 17:32:21 +0100 Received: from camex21.campus.fu-berlin.de ([130.133.170.205]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES256-GCM-SHA384:256) (envelope-from ) id <1iufP3-003daQ-0S>; Thu, 23 Jan 2020 17:32:21 +0100 Received: from camex21.campus.fu-berlin.de (130.133.170.205) by camex21.campus.fu-berlin.de (130.133.170.205) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.1591.10; Thu, 23 Jan 2020 17:32:19 +0100 Received: from camex21.campus.fu-berlin.de ([fe80::f433:2f2d:6328:c05f]) by camex21.campus.fu-berlin.de ([fe80::f433:2f2d:6328:c05f%3]) with mapi id 15.01.1591.012; Thu, 23 Jan 2020 17:32:19 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: SeqAn Development Thread-Topic: [Seqan-dev] SeqAn Release 3.0.1 Thread-Index: AQHV0TH7Zrgie6srbEixstozhwpsiqf261MAgAF24AA= Message-ID: References: <0a33b094aaa149b1b72041f2399141d2@fu-berlin.de> In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-ID: <2EF5AE1CFEA4444D899C4EDFD52B6869@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 23 Jan 2020 17:32:19 +0100 X-Original-Date: Thu, 23 Jan 2020 16:32:19 +0000 X-Originating-IP: 130.133.170.205 X-Original-X-Originating-IP: [130.133.175.152] X-ZEDAT-Hint: X X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1579797141-0002E834-AC894685/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.444702, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.3 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn Release 3.0.1 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 23 Jan 2020 16:32:22 -0000 Dear Diaa Fayed, thank you very much for writing us. We appreciate your feedback. Can I ask you if there are features you are missing in particular?=20 The goal of SeqAn3 is to reduce the code complexity with the help of modern= C++, while still providing cutting edge algorithms and data structures for= the bioinformatics community. The implied changes to an existing program might be overwhelming at first b= ut we believe there is a long-term benefit from that.=20 Some of these benefits include that errors are easier to track, coding can = be much faster through easier interfaces and less boiler plate code and our= design goes well with new features from the standard library to get the mo= st out of your tools.=20 The other reason is that SeqAn2 has reached its end-of-life. There will lik= ely be a last bug-fix release that improves compatibility with SeqAn3, but = I am afraid that no further resources can be invested into keeping it up to= date or fixing newly-found issues. Regarding the advanced C++ concepts that are fairly new: We are going to pr= ovide more and more teaching materials as well as try to be around on confe= rences to teach those concepts and introduce features of the library. We wi= ll inform you via our channels of any of those opportunities.=20 Of course, we have to admit that at the moment not all interfaces or featur= es are complete and that it might be that some interfaces might change unti= l 3.1 is fixed.=20 On the other hand we'd like to hear from the community what their experienc= e with the new library is so we can learn from them, improve the interfaces= and provide a better high-quality and sustainable software for the communi= ty.=20 So if you are critical of these changes, we would be particularly intereste= d in your feedback if you do have the chance to try out SeqAn3! Yours sincerely, The SeqAn Team > On 22. Jan 2020, at 19:10, Diaa Fayed wrote: >=20 > - I read about both SeqAn3 and SeqAn2. > - Documentation and some algorithms have not implemented yet in SeqAn3 > - SeqAn3 is based on very advanced C++ concepts I have not known about y= et >=20 > so >=20 > I prefer to use SeqAn2.4 >=20 > what is your opinion? > -------------------------------------------------------------------------= ----------------------- >=20 > On 1/22/20, Seiler, Enrico Frank wrote: >> We are excited to present a new update of our SeqAn library. This releas= e >> has been in the making for roughly half a year now and we are proud to >> present some great new features and also a lot of improvements with resp= ect >> to runtime and usability. You can find a comprehensive list of the chang= es >> in our >> changelog. >>=20 >> * Get to know SeqAn3 with our >> tutorials. >> * Visit our API >> documentation. >> * See the porting >> guide for s= ome >> help on porting from SeqAn2. >>=20 >> Note that 3.1.0 will be the first API stable release and interfaces in t= his >> release might still change. >> [tada] Notable new features >>=20 >> * >> We added support for type erasing >> semialphabets >> that allows you to manage semialphabets with the same alphabet size in o= ne >> container. This can have a big effect on your compile-time, in case you >> don't drink as much [coffee] as we do. >> * >> We added parallel support for the alignment algorithm. You can now confi= gure >> the number of threads you want to use for the alignment computation. >> * >> One to command them all: Our argument parser now supports subcommands, s= uch >> as git pull. A >> How-to will >> guide you through setting this up for your tool. >> * >> The performance of the I/O was improved to allow faster file reading. >> Further, we added support for reading and writing the CIGAR string throu= gh >> alignment files. >> * >> We added several new ranges and views. Most notably, the >> seqan3::views::kmer_hash view, which transforms a sequence into a range = of >> k-mer hashes efficiently. Another view of great practice is the >> seqan3::views::to, which can be used to convert a view into a container.= We >> also added aseqan3::dynamic_bitset which is a dynamic version of the >> std::bitset. >> * >> Memory consumption of the (bidirectional) FM-Index for text collections = was >> reduced by 10%. >>=20 >> [:trollface:] Notable API changes >> As much as we'd like to reduce inconsistencies between releases, we are >> sometimes forced to change an interface either to improve usability or t= o >> follow changes made by the ISO C++ committee. >>=20 >> * All our concepts are named in the snake_case style (e.g. >> seqan3::WritableAlphabet -> seqan3::writable_alphabet)! >> * The directory seqan3/range/view has been renamed to >> seqan3/range/views. >> * The namespace seqan3::view has been renamed to seqan3::views. >> * The CMake variable SEQAN3_VERSION_STRING defined by >> find_package(SEQAN3) was renamed to SEQAN3_VERSION. >>=20 >> You can find a comprehensive list of the changes in our >> changelog. >> [bug] Notable bug fixes >>=20 >> * Copying and moving the seqan3::fm_index and seqan3::bi_fm_index now >> work properly. >> * The translation table for nucleotide to amino acid translation was >> corrected. >> * The amino acid score matrices were corrected. >>=20 >> [electric_plug] External dependencies >>=20 >> * We now support ranges-v3 versions >=3D 0.10.0 and < 0.11.0, increas= ing >> the previous requirement of >=3D 0.5.0 and < 0.6.0. >> * We now support cereal version 1.3.0, increasing the previous >> requirement of 1.2.2 >>=20 >>=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From dr.diaafayed@gmail.com Fri Jan 24 06:59:17 2020 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:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iurzw-003gI1-CY>; Fri, 24 Jan 2020 06:59:16 +0100 Received: from mail-wr1-f41.google.com ([209.85.221.41]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (envelope-from ) id <1iurzw-00304p-8c>; Fri, 24 Jan 2020 06:59:16 +0100 Received: by mail-wr1-f41.google.com with SMTP id b6so556095wrq.0 for ; Thu, 23 Jan 2020 21:59:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :content-transfer-encoding; bh=YCjqWL978FQdi1/EFn500tTP25MtQ85tpWlib2O5gHs=; b=quDBTHC/VX70WLaCpjK/rGoRpcY3tLVGsWh9mrGIRwLVd9TCzSp45ca9W1ZM8nTCvp TJeAPCaFhq4pN/ZOt9dVwCyNMf8e3ygZRk+vLMYd97XoKWmbISPaYYiLuXN/A4O13byH ah1c0nGQb7+iuv1TyhWEtxAid/H3wZGq/1caN2SYw5EJYoIo491kudDt3Ca8t+4dkZcA 2W/fh2mwHFzdsi8aAdQOCjluOtbYQ4LMMCCrb7aXr+wgWwHreWI3khXRpcIy3fEuXDgJ TraUe/zxcI53EZi8GpaPnMnwAHS+kNq4TLiDUZEUfFnEeDDj+Z37SVAVvtM/GGkruK19 o25Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:content-transfer-encoding; bh=YCjqWL978FQdi1/EFn500tTP25MtQ85tpWlib2O5gHs=; b=MRn/W909fPWKsbcRdMOcDTC9ugJXSb9/H8ti2RYUgBnW3NflXOpx5zkGGFP9wPjXGX 7VTYQx6zBFN7nnPJ63xIap7sPLsNW9ZPzx5f0XAcqym06bCq8tpJI3wVabdeDJiXUEoI RIsPcqYsPD5cjKt1zolkTINZ69cyezwhJvZjT2+oe5qPrvrGFJNMb3PKrbK+STHU1UTJ OJGCRPeg3qfJRaT1UxzzsMhTWjoUA7LOSVcCPPv8/+I/xrRXCDagek8X4OmKNqo0Natp L/GH6xVKpgCkPp7V82QZESYriffVquMLckjU9Spajr2ZybHMx0k3eWMd4cFOTxK0oCLp ev5Q== X-Gm-Message-State: APjAAAXmKoJA9558AEcoBKFtdT+Eiel0m/B9XzYRJdHRSBU8sytLSOV+ 7c7jscTgmX7KGy6mbTjfjVQr1FvAtERDcQBytT5mgg== X-Google-Smtp-Source: APXvYqwpPu4xlBo8LOp0ozEg1yoDO1J1PIR/K4YM0uaUW9heNVJog0AyOJzAyvZjSPYQhf+i33WhKNbgSY/ZKewApM4= X-Received: by 2002:a5d:6346:: with SMTP id b6mr2105802wrw.354.1579845554463; Thu, 23 Jan 2020 21:59:14 -0800 (PST) MIME-Version: 1.0 Received: by 2002:a05:600c:21a:0:0:0:0 with HTTP; Thu, 23 Jan 2020 21:59:13 -0800 (PST) In-Reply-To: References: <0a33b094aaa149b1b72041f2399141d2@fu-berlin.de> From: Diaa Fayed Date: Fri, 24 Jan 2020 07:59:13 +0200 Message-ID: To: SeqAn Development Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Originating-IP: 209.85.221.41 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1579845556-000B5AFF-ED23362B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.476852, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_FROM,RCVD_IN_DNSWL_NONE, RCVD_IN_MSPIKE_H2,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.3 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] SeqAn Release 3.0.1 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 24 Jan 2020 05:59:17 -0000 Thanks very much - I hope the problems will be solved soon - some bugs -- .. the semaphore.h file missed -- when running on Windows and Code::Blocks or on Cygwin On 1/23/20, Rahn, Ren=C3=A9 wrote: > Dear Diaa Fayed, > > thank you very much for writing us. We appreciate your feedback. > Can I ask you if there are features you are missing in particular? > > The goal of SeqAn3 is to reduce the code complexity with the help of mode= rn > C++, while still providing cutting edge algorithms and data structures fo= r > the bioinformatics community. > The implied changes to an existing program might be overwhelming at first > but we believe there is a long-term benefit from that. > Some of these benefits include that errors are easier to track, coding ca= n > be much faster through easier interfaces and less boiler plate code and o= ur > design goes well with new features from the standard library to get the m= ost > out of your tools. > The other reason is that SeqAn2 has reached its end-of-life. There will > likely be a last bug-fix release that improves compatibility with SeqAn3, > but I am afraid that no further resources can be invested into keeping it= up > to date or fixing newly-found issues. > > Regarding the advanced C++ concepts that are fairly new: We are going to > provide more and more teaching materials as well as try to be around on > conferences to teach those concepts and introduce features of the library= . > We will inform you via our channels of any of those opportunities. > > Of course, we have to admit that at the moment not all interfaces or > features are complete and that it might be that some interfaces might cha= nge > until 3.1 is fixed. > On the other hand we'd like to hear from the community what their experie= nce > with the new library is so we can learn from them, improve the interfaces > and provide a better high-quality and sustainable software for the > community. > > So if you are critical of these changes, we would be particularly interes= ted > in your feedback if you do have the chance to try out SeqAn3! > > Yours sincerely, > > The SeqAn Team > >> On 22. Jan 2020, at 19:10, Diaa Fayed wrote: >> >> - I read about both SeqAn3 and SeqAn2. >> - Documentation and some algorithms have not implemented yet in SeqAn3 >> - SeqAn3 is based on very advanced C++ concepts I have not known about >> yet >> >> so >> >> I prefer to use SeqAn2.4 >> >> what is your opinion? >> ------------------------------------------------------------------------= ------------------------ >> >> On 1/22/20, Seiler, Enrico Frank wrote: >>> We are excited to present a new update of our SeqAn library. This >>> release >>> has been in the making for roughly half a year now and we are proud to >>> present some great new features and also a lot of improvements with >>> respect >>> to runtime and usability. You can find a comprehensive list of the >>> changes >>> in our >>> changelog. >>> >>> * Get to know SeqAn3 with our >>> tutorials. >>> * Visit our API >>> documentation. >>> * See the porting >>> guide for >>> some >>> help on porting from SeqAn2. >>> >>> Note that 3.1.0 will be the first API stable release and interfaces in >>> this >>> release might still change. >>> [tada] Notable new features >>> >>> * >>> We added support for type erasing >>> semialphabets >>> that allows you to manage semialphabets with the same alphabet size in >>> one >>> container. This can have a big effect on your compile-time, in case you >>> don't drink as much [coffee] as we do. >>> * >>> We added parallel support for the alignment algorithm. You can now >>> configure >>> the number of threads you want to use for the alignment computation. >>> * >>> One to command them all: Our argument parser now supports subcommands, >>> such >>> as git pull. A >>> How-to wil= l >>> guide you through setting this up for your tool. >>> * >>> The performance of the I/O was improved to allow faster file reading. >>> Further, we added support for reading and writing the CIGAR string >>> through >>> alignment files. >>> * >>> We added several new ranges and views. Most notably, the >>> seqan3::views::kmer_hash view, which transforms a sequence into a range >>> of >>> k-mer hashes efficiently. Another view of great practice is the >>> seqan3::views::to, which can be used to convert a view into a container= . >>> We >>> also added aseqan3::dynamic_bitset which is a dynamic version of the >>> std::bitset. >>> * >>> Memory consumption of the (bidirectional) FM-Index for text collections >>> was >>> reduced by 10%. >>> >>> [:trollface:] Notable API changes >>> As much as we'd like to reduce inconsistencies between releases, we are >>> sometimes forced to change an interface either to improve usability or >>> to >>> follow changes made by the ISO C++ committee. >>> >>> * All our concepts are named in the snake_case style (e.g. >>> seqan3::WritableAlphabet -> seqan3::writable_alphabet)! >>> * The directory seqan3/range/view has been renamed to >>> seqan3/range/views. >>> * The namespace seqan3::view has been renamed to seqan3::views. >>> * The CMake variable SEQAN3_VERSION_STRING defined by >>> find_package(SEQAN3) was renamed to SEQAN3_VERSION. >>> >>> You can find a comprehensive list of the changes in our >>> changelog. >>> [bug] Notable bug fixes >>> >>> * Copying and moving the seqan3::fm_index and seqan3::bi_fm_index no= w >>> work properly. >>> * The translation table for nucleotide to amino acid translation was >>> corrected. >>> * The amino acid score matrices were corrected. >>> >>> [electric_plug] External dependencies >>> >>> * We now support ranges-v3 versions >=3D 0.10.0 and < 0.11.0, >>> increasing >>> the previous requirement of >=3D 0.5.0 and < 0.6.0. >>> * We now support cereal version 1.3.0, increasing the previous >>> requirement of 1.2.2 >>> >>> >> >> _______________________________________________ >> 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 >