From wmueller4711@me.com Mon Nov 18 12:17:40 2019 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 <1iWf2G-001fSS-86>; Mon, 18 Nov 2019 12:17:36 +0100 Received: from mr85p00im-zteg06011501.me.com ([17.58.23.182]) by relay1.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 <1iWf2G-0008E3-0a>; Mon, 18 Nov 2019 12:17:36 +0100 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=me.com; s=1a1hai; t=1574075852; bh=qMYQ+KqRd/wolHI3vPa7sR6MHSVu0/KOMnKbjNazCYA=; h=From:Content-Type:Subject:Message-Id:Date:To; b=Oa2wzP4LHY89Sa2WuEPup+0t9swA+yLoebtrx4wScE6fklfDzNc6P+Kr/QM7V4u+J NDbcLe2hUiH2SQrKxL1vzddzXdQhuTLw0QYK5v3gM97AIPiIma0knDCpJejBWq99wj z8EQVW8yJrLXBpPH7XygzrnZ7/5251MWu+fxQL/3hEHiEETzWjjQt2B6PC5VuRSZL6 JmYSnRitpvD5bQ0Ck1ikoWzDs2V9my5PZEuYYUFNiae1Ok0vUnjEbrx/ltSVsHb3L/ vzg0sJAApG/zxHnyEpfuu+71aRakPYO+MhVSVawkFzzjxGtcj51YfE4XgRuYdeYvYA k1pxk0ykAlj3g== Received: from werners-mbp.fritz.box (cable-84-44-203-212.nc.de [84.44.203.212]) by mr85p00im-zteg06011501.me.com (Postfix) with ESMTPSA id 05F342A08E9 for ; Mon, 18 Nov 2019 11:17:31 +0000 (UTC) From: =?utf-8?Q?Werner_M=C3=BCller?= Content-Type: multipart/alternative; boundary="Apple-Mail=_B0473549-3CC8-4540-85E3-23DD0FE80017" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Message-Id: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> Date: Mon, 18 Nov 2019 12:17:29 +0100 To: seqan-dev@lists.fu-berlin.de X-Mailer: Apple Mail (2.3445.104.11) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:, , definitions=2019-11-18_02:, , signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=1 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1011 mlxscore=0 mlxlogscore=521 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-1908290000 definitions=main-1911180103 X-Originating-IP: 17.58.23.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574075856-000256AF-F54660B2/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.027233, 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,DKIM_VALID_EF,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM, HTML_MESSAGE,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Home brew installation error message 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: Mon, 18 Nov 2019 11:17:40 -0000 --Apple-Mail=_B0473549-3CC8-4540-85E3-23DD0FE80017 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii homebrew/science was deprecated. This tap is now empty as all its = formulae were migrated. Most likely you need to move it to a new directory.= --Apple-Mail=_B0473549-3CC8-4540-85E3-23DD0FE80017 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
homebrew/science was deprecated. This tap is now empty as all = its formulae were migrated.

Most likely you need to move it to a new = directory.
= --Apple-Mail=_B0473549-3CC8-4540-85E3-23DD0FE80017-- From wmueller4711@me.com Mon Nov 18 13:16:42 2019 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 <1iWfxS-001lNf-3P>; Mon, 18 Nov 2019 13:16:42 +0100 Received: from mr85p00im-ztdg06021201.me.com ([17.58.23.189]) by relay1.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 <1iWfxR-000VEu-Nc>; Mon, 18 Nov 2019 13:16:42 +0100 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=me.com; s=1a1hai; t=1574079398; bh=WSfhqh3jXj1mvPiYXxi/QzbaOum6c/bWaTfi/Z+i+i4=; h=From:Content-Type:Subject:Date:To:Message-Id; b=rpU+9HQh4QekayBPKog3cwR8PDaQzJp39ApoRo47onahjpxN6ZqPa9rR9jn4isJ6S iRfxcpHmA0AjUdWOuANr4x7wDq0r03+8P1JedFg3Lsx+BN5hwc5ACp4EAJc+OfOoZg aVvcNOkugtupVXqf7zLklqNOem6V2xbwuo2Ak0EeVCt04L1dam1Xm7r6Tc2dqxJ4+p RDSd1B43gAn//hckGUPpSI+eji+TZMz7jg7qEljbhrsydjL5fzcKnWBZ3marhkkiFm KdyosHgMDjDJKssdntJUCZKFHBOqF7BEm7xywAQirOy6Mu2gzMQ2mGNI4fCIxGrXbX jponwPgJaFf6A== Received: from werners-mbp.fritz.box (cable-84-44-203-212.nc.de [84.44.203.212]) by mr85p00im-ztdg06021201.me.com (Postfix) with ESMTPSA id 711391208CF for ; Mon, 18 Nov 2019 12:16:38 +0000 (UTC) From: =?utf-8?Q?Werner_M=C3=BCller?= Content-Type: multipart/alternative; boundary="Apple-Mail=_BCB45CDF-C585-4517-A060-AD1567A1C00A" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Date: Mon, 18 Nov 2019 13:16:36 +0100 References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> To: SeqAn Development In-Reply-To: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> Message-Id: <1723D540-DB75-45AE-A87B-950B8ACB3D32@me.com> X-Mailer: Apple Mail (2.3445.104.11) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:, , definitions=2019-11-18_02:, , signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1015 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-1908290000 definitions=main-1911180113 X-Originating-IP: 17.58.23.189 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574079402-000256AF-565BB16A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.042350, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.6 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM, HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Home brew installation error message 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: Mon, 18 Nov 2019 12:16:42 -0000 --Apple-Mail=_BCB45CDF-C585-4517-A060-AD1567A1C00A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 May be best would be to use brewsci/bio ? ----- Here is the information from the homebrew page: Homebrew/science (deprecated) These formulae provided software tailored to scientific endeavours. This tap was deprecated because it had different goals from the wider = Homebrew organisation (e.g. Linuxbrew CI/support). All widely used, = buildable formulae were migrated to homebrew/core. If you wish to migrate other widely used formulae = to = Homebrew/homebrew-core please submit a pull request = there. You may be interested in the brewsci/bio = and brewsci/science = taps. > On 18 Nov 2019, at 12:17, Werner M=C3=BCller = wrote: >=20 > homebrew/science was deprecated. This tap is now empty as all its = formulae were migrated. >=20 > Most likely you need to move it to a new directory. > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_BCB45CDF-C585-4517-A060-AD1567A1C00A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
May be best would be to use brewsci/bio ?


-----

Here is the = information from the homebrew page:

Homebrew/science (deprecated)

These formulae provided software tailored to = scientific endeavours.

This= tap was deprecated because it had different goals from the wider = Homebrew organisation (e.g. Linuxbrew CI/support). All widely used, = buildable formulae were migrated to homebrew/core.

If you wish to migrate other widely used = formulae to Homebrew/homebrew-core please submit a pull = request there.

You may be interested in the brewsci/bio and brewsci/science taps.

On 18 = Nov 2019, at 12:17, Werner M=C3=BCller <wmueller4711@me.com>= wrote:

homebrew/science was deprecated. This = tap is now empty as all its formulae were migrated.

Most likely you need to move it to a new = directory.
_____________________________________________= __
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

= --Apple-Mail=_BCB45CDF-C585-4517-A060-AD1567A1C00A-- From wmueller4711@me.com Mon Nov 18 13:32:54 2019 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 <1iWgD7-001n9q-NM>; Mon, 18 Nov 2019 13:32:53 +0100 Received: from mr85p00im-ztdg06011201.me.com ([17.58.23.181]) by relay1.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 <1iWgD7-000cA1-B5>; Mon, 18 Nov 2019 13:32:53 +0100 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=me.com; s=1a1hai; t=1574080370; bh=jZ2eb9rMEmCEeM92saZ7KcwJIEYRSSgFqLFcb6SDL9E=; h=From:Content-Type:Subject:Date:To:Message-Id; b=i66aa//9FzPYaH/qFQIkHZQS7jxYUW5pR8YerIZ/ayIO7NvVf25eMJu6c1ElEPHhP /Rh0uvvatG78qul3/AQ1dBcaGr7wt34KJvagEDL5MvbK8PAwbxaHPtcx9m2mK3F6d3 ssHwdMKM2LS+Koiwb13qn0hSEUSBuu3NXr7ykHmAj7t2P2UTPC5IcdQoXr14lRcU1k NC6Qn8kuBrVAcNR0g46bEl12xptO4A1sycFLygXAVKrNrGg5R1i7C1SyXlLtfSn6fx P3osTntuXM22zc2PqxYw3ftl31x7B48Kk0iMR3HFnqt9T65AZdXRZ++2y+799wlbn9 THTrtJBCdep9Q== Received: from werners-mbp.fritz.box (cable-84-44-203-212.nc.de [84.44.203.212]) by mr85p00im-ztdg06011201.me.com (Postfix) with ESMTPSA id 13733400E97 for ; Mon, 18 Nov 2019 12:32:49 +0000 (UTC) From: =?utf-8?Q?Werner_M=C3=BCller?= Content-Type: multipart/alternative; boundary="Apple-Mail=_2CFFFBCC-7FE4-42F9-969A-DC3A8CF4F10B" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Date: Mon, 18 Nov 2019 13:32:47 +0100 References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> To: SeqAn Development In-Reply-To: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> Message-Id: <5412AD17-D608-4B47-BA58-F4B3C073BED0@me.com> X-Mailer: Apple Mail (2.3445.104.11) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:, , definitions=2019-11-18_02:, , signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1015 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-1908290000 definitions=main-1911180115 X-Originating-IP: 17.58.23.181 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574080373-000256AF-6E5B6696/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000160, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.6 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM, HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Home brew installation error message 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: Mon, 18 Nov 2019 12:32:54 -0000 --Apple-Mail=_2CFFFBCC-7FE4-42F9-969A-DC3A8CF4F10B Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Homebrew seqan brew install homebrew/science/seqan info = | = contact Info and contact links are broken. > On 18 Nov 2019, at 12:17, Werner M=C3=BCller = wrote: >=20 > homebrew/science was deprecated. This tap is now empty as all its = formulae were migrated. >=20 > Most likely you need to move it to a new directory. > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_2CFFFBCC-7FE4-42F9-969A-DC3A8CF4F10B Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Homebrewseqanbrew install homebrew/science/seqaninfo | contact
Info and = contact links are broken.

On 18 Nov 2019, at 12:17, = Werner M=C3=BCller <wmueller4711@me.com> wrote:

homebrew/science was deprecated. This = tap is now empty as all its formulae were migrated.

Most likely you need to move it to a new = directory.
_____________________________________________= __
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

= --Apple-Mail=_2CFFFBCC-7FE4-42F9-969A-DC3A8CF4F10B-- From lijin.abc@gmail.com Sat Nov 23 22:58:17 2019 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 <1iYdPw-002SED-LO>; Sat, 23 Nov 2019 22:58:12 +0100 Received: from mail-io1-f54.google.com ([209.85.166.54]) 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 <1iYdPw-003Lv9-EI>; Sat, 23 Nov 2019 22:58:12 +0100 Received: by mail-io1-f54.google.com with SMTP id u24so10263357iob.5 for ; Sat, 23 Nov 2019 13:58:11 -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=txvwLj4u98ThMPQmttnJlMXSvyEM3staHE14pqwMe3E=; b=OaXX2GfEpLtjaUXXSVO50aXTI4NoqTXRyXPsfHXBjQp79Lcs1G38chtg7mb9W/biep QpFKeuzv+mjJTFhgYZ8SBatxPUnzyq4zaNDNu75KlrQWcXT2AJ9jzRjAheQszzJ0nUXu /mnYXLCFHNZcbmPRisLXFRwJbLoXWPZRWUdM3QPJulp54Tnh8pVf1VzyR/4mDeA0y6nQ txik1a5srRd1kPuh8K633nNmCk2tXyhRDl9GC5Qj+ml9QQpxvgnKDA7L2lYQfJOWFHgv 09qnOuNTczMdkHdtihtydRtGi4gvvWUdRerhZOmA5kvsYwurA6FDOh2bzlU5ownf8A8S fIMw== 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=txvwLj4u98ThMPQmttnJlMXSvyEM3staHE14pqwMe3E=; b=S3j+7hJIQ/FWgW9Gkwpvc3R/8taSbQdayDWHwWEjv1R8YcydXr/aPsUEyr/RYK4Hlb N3PLxBGUyT2PCP0nj0UNzueC2M3wgj0Ao6Pi0PX5M04qi+vBDDgrEJPj04m7tTzZfkrN MhAqQXwk8Iw+TJUuo5gr0JLaGVuND6AVtre8AxgV9OH+QMH3YqxCMq5v2s5MVm6HW/Nv E7oVWOepfuoJdjXMHAOFNU5eJ/w4u9+8G3ObSNVn2mzepN9d6zYHoCaKxVI/MNWG48AJ ZgEdLB8dXCcPeTdENS9q463trla/cNlhat01yv/15lpLSJNZZCJT0BzRTQcVg5Rh/neR LMJA== X-Gm-Message-State: APjAAAWdF6jF/OR6XcuKmp3APUOs0S2fMiIn+fmdnlEydA1WsFtXpCPY j4Bfh9gIa//wZv2MoGjorimfL2gLAV1NB2J2BMoFmIm4ArA= X-Google-Smtp-Source: APXvYqzL6WYWu63jzsWKS34/AJcr0F3fHmpet72EDpT2c7Fs0afWq71DfDiVM06J8An5UPg6bq4nfMDwbR3vlvbM7Xg= X-Received: by 2002:a02:aa14:: with SMTP id r20mr20672346jam.19.1574546289504; Sat, 23 Nov 2019 13:58:09 -0800 (PST) MIME-Version: 1.0 From: Jin Li Date: Sat, 23 Nov 2019 15:57:58 -0600 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset="UTF-8" X-Originating-IP: 209.85.166.54 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574546292-00026DE6-84EC7BC1/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.332845, 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_MSPIKE_H2, SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] To read chromosome-specific records from a BAM file using SeqAn3. 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: Sat, 23 Nov 2019 21:58:17 -0000 Hi all, I want to read a BAM file for chromosome-specific records using the BAM index information so that I don't need to go through the whole BAM file. For example, I want to extract alignment records in chr17 only. Can you help point out the way for this speedup reading using SeqAn3? Thank you. Best regards, Jin From lijin.abc@gmail.com Sat Nov 23 22:59:24 2019 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 <1iYdR5-002SKD-Nc>; Sat, 23 Nov 2019 22:59:23 +0100 Received: from mail-il1-f182.google.com ([209.85.166.182]) 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 <1iYdR5-003MIH-HB>; Sat, 23 Nov 2019 22:59:23 +0100 Received: by mail-il1-f182.google.com with SMTP id g12so1240518ild.2 for ; Sat, 23 Nov 2019 13:59:22 -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=Dized52UQoe2O21zMwvkz7y1HpUfaV8IxHWcdMXEhZE=; b=DrhFlyO/s6/yv/EcER+L8oos0q9QBF4ClcKQZSvn84qNUUgm122An2OYYaJzxbpxdy QlrRuzMT6/qbxjGzF6S4C1U6z/Ss56TWEejXRkTeFywi5kuFVuYaUNCXTC3CRh47uf24 lX96HxpmR5yYMepqAbUHlDAZygszDJcf1+d69oNNLbGN2swZBMw31hCsMf9y9/6TTWtc x7OOdrhp2K38WPvrZHQmCaS3AvCpHtYakxQvRrLZ5dLLX9B47LEqxyiftO9kmfVt3zvA vVIkGP3BUTpW2FKyJzvP7RHl1rvnViYVRSSR0RoZUoHv/W9BcSGYByr4/4ERL86QGFDQ WSdg== 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=Dized52UQoe2O21zMwvkz7y1HpUfaV8IxHWcdMXEhZE=; b=OAi1UB7InqMi8vEDkxmcBunl2BEIuZIZBBXCgdaFMv+0fqbsB7gvUexu1WBCtwYpcc NXsHl2/ZO5JnC+YwSPmTIIWlCuIGEqjin45KsYHifXnIoeVDU31RM04YmnFos3p566vT 2Px+W1VcuX3IeKOPOWboPd4aqaYmwXHpJQoD0E8CErKLgCMrBVSC2ORI+PPpjUOmBWlG VaCFxmMw6Uv7uWerl3NHWO5x6eCWV5AZrKIxP3rp/nBYOoTizgETMsBdkXOp9scQkjd4 94GZQGNUyyWKGNg5vrbGFLUWPb551x1Py+hNz6qsC8lKhyFlspQgucD2UHHrM1lfmuHg SoAQ== X-Gm-Message-State: APjAAAVFpwyseXX3Sr/ni2n28Fdd/VHmxhcxld3ZpjnEFt2CLmWgzSWL 5C1Ppw9IqtR74gMg3DUTXDEhX8RQZFV/tJm/TueY57Mm5og= X-Google-Smtp-Source: APXvYqxVFphRQTruoUZBBSE9mdBojcbJ1GDgpva3aUmdoK2YmDastCOKymAHHi+WdsP4FarwohG3o8rkFkCvuJq418Y= X-Received: by 2002:a92:aa48:: with SMTP id j69mr25596269ili.162.1574546360875; Sat, 23 Nov 2019 13:59:20 -0800 (PST) MIME-Version: 1.0 From: Jin Li Date: Sat, 23 Nov 2019 15:59:10 -0600 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset="UTF-8" X-Originating-IP: 209.85.166.182 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574546363-00026DE6-A12A763F/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.363566, 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 3.4.2 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Demos to extract references from the BAM header using SeqAn3. 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: Sat, 23 Nov 2019 21:59:24 -0000 Hi all, I am trying to use SeqAn3 to read reference names (e.g. chr1, chr2, xxx) from the BAM header quickly. However, I can not find a clear demonstration of this task. Can you help point out the demos? Thank you for your help. Best regards, Jin From lijin.abc@gmail.com Sat Nov 23 23:09:05 2019 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 <1iYdaP-002TF0-TQ>; Sat, 23 Nov 2019 23:09:02 +0100 Received: from mail-il1-f172.google.com ([209.85.166.172]) 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 <1iYdaP-003QMb-Mw>; Sat, 23 Nov 2019 23:09:01 +0100 Received: by mail-il1-f172.google.com with SMTP id a7so10691009ild.6 for ; Sat, 23 Nov 2019 14:09:00 -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=1Vfq2JTDMjuwO5uEvctH9GGSLDsxyqnQYxMXtjfhhPA=; b=Y0EW3+CfAKfdFOJE73hFAhhzyPkCCUautVB4+yhQMvufW0oxqx6bjU3Y6omKWReUyX qtiZe7ahZYy4NB324WmUHDvmcKRGdgo+0X6aNC0osKUU//j/23yMiCpbDDvVnpQO2Ddi Rkfu0cXpRU+MZ2CcSdzqYiAZKQ5t5MAbUor7RBi1ekaWmqKtFbeEtMtkN952KjYrAkuY KeoL/iWom7WaFq8/42UuLCiidGZJUH4ywpzSTpiLG3/Du3LAtpcbMW+MQqXKk6HzBbmf 9mz4gKxEatHtLckm/mybUGaoqR2AeEdqnWsEhULs5uVwgeyYm2qyEZLl/QeiiPQBelku zh0A== 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=1Vfq2JTDMjuwO5uEvctH9GGSLDsxyqnQYxMXtjfhhPA=; b=fyKAjMEWRiVrTCxqgDcMSgPFZtOuXy/KbBRcbDhOV23Ox44YluX9L77Y28VnO9RoBm TGgJwsZCW7eFTsoch//SFoqyQFVTH0+MVtAtO9IDR9gokrgzJIQDiYbXaPhzPfoSH7yp FxDR55AltZ0nL8PDns1XmGI5RPxopY9MMz9Ymtm8Fziw6bQ0hD3SXQbeoJXFhMy1LBPW 0kOPbYMfl9BwGRMfFi/y0UPpHzV8lnLYZj+oR9wPbUXg89Dm3f2UZchQidENPu3ApY79 vkaukVsOnqPgYWeI+FUBBX+wL/MVX+CdmkT9EvJBw/8UDEmmO/cspqJU56hdaZqSRK5i vThg== X-Gm-Message-State: APjAAAVRaQ2GekvAm2ZqfMtHglwm7lNcYSKlM4X+VvO7IodpGv5m0k9F t76zWEK34p+swTLoEr0Dk5h8b1PWIMjc8O9KAEhp4517qfk= X-Google-Smtp-Source: APXvYqzQ5+4OVRbN3gQPS0xm4tQ7CpTbymmYoF5AW0sqNoTlfF+teXeJ98bHX7W7nT8MYCBpZo/aMUZ6sXaSkSDQO9w= X-Received: by 2002:a92:ce03:: with SMTP id b3mr23635334ilo.179.1574546939278; Sat, 23 Nov 2019 14:08:59 -0800 (PST) MIME-Version: 1.0 From: Jin Li Date: Sat, 23 Nov 2019 16:08:48 -0600 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset="UTF-8" X-Originating-IP: 209.85.166.172 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574546941-00026DE6-C3FF9F88/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.255181, 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_MSPIKE_H2, SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] The definition of classes in SeqAn2. 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: Sat, 23 Nov 2019 22:09:06 -0000 Hi all, I am trying to adapt SeqAn2 in my program. I have a problem to find out class definitions in SeqAn2. For example, in the following tutorial, https://seqan.readthedocs.io/en/master/Tutorial/InputOutput/SamAndBamIO.html#accessing-the-header `TBamContext` is used to define a variable for header information, and I want to extract the reference names (such as chr1, chr2, xxx) from it, and save them as std::string in native C++. However, the class's definition is not clear, and the interfaces for the conversion are not directly available either. Can you help point out documentation about these class type definitions in SeqAn2? Thank you. Best regards, Jin From hannes.hauswedell@fu-berlin.de Mon Nov 25 11:16:05 2019 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:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBPY-001hDY-N2>; Mon, 25 Nov 2019 11:16:04 +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:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBPY-000sbT-Kw>; Mon, 25 Nov 2019 11:16:04 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.38.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) with esmtpsa (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBPY-003tOa-Dp>; Mon, 25 Nov 2019 11:16:04 +0100 From: Hannes Hauswedell To: rene.rahn@fu-berlin.de Cc: seqan-dev@lists.fu-berlin.de, Werner =?ISO-8859-1?Q?M=FCller?= Date: Mon, 25 Nov 2019 11:16:05 +0100 Message-ID: <5181197.8gLySxXtyI@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <5412AD17-D608-4B47-BA58-F4B3C073BED0@me.com> References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> <5412AD17-D608-4B47-BA58-F4B3C073BED0@me.com> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.38.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574676964-0002BF59-FA87A1BD/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 X-Spam-Checker-Version: SpamAssassin 3.4.2 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Home brew installation error message 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: Mon, 25 Nov 2019 10:16:05 -0000 Rene, can you take care of this? Am Montag, 18. November 2019, 13:32:47 CET schrieb Werner M=C3=BCller: > Homebrew seqan brew install homebrew/science/seqan info > | > contact Info and contact links are broken. >=20 > > On 18 Nov 2019, at 12:17, Werner M=C3=BCller wrot= e: > >=20 > > homebrew/science was deprecated. This tap is now empty as all its formu= lae > > were migrated. > >=20 > > Most likely you need to move it to a new directory. > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev =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 From Rene.Rahn@fu-berlin.de Mon Nov 25 11:19:48 2019 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 <1iZBTA-001hcZ-3f>; Mon, 25 Nov 2019 11:19:48 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBTA-000u8o-0f>; Mon, 25 Nov 2019 11:19:48 +0100 Received: from camex23.campus.fu-berlin.de ([130.133.170.207]) by relay2.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:AES256-GCM-SHA384:256) (envelope-from ) id <1iZBT9-002Q4m-Ls>; Mon, 25 Nov 2019 11:19:47 +0100 Received: from camex21.campus.fu-berlin.de (130.133.170.205) by camex23.campus.fu-berlin.de (130.133.170.207) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.1591.10; Mon, 25 Nov 2019 11:19:45 +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; Mon, 25 Nov 2019 11:19:45 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: "Hauswedell, Hannes" CC: SeqAn Development , =?utf-8?B?V2VybmVyIE3DvGxsZXI=?= Thread-Topic: [Seqan-dev] Home brew installation error message Thread-Index: AQHVngHem8SiPj7cx0aC/HNCmAtdkaeQy8mAgAraIICAAAEHgA== Message-ID: <453DCC98-9E0E-42B3-9FC7-1018FCACF8BA@fu-berlin.de> References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> <5412AD17-D608-4B47-BA58-F4B3C073BED0@me.com> <5181197.8gLySxXtyI@celegans.imp.fu-berlin.de> In-Reply-To: <5181197.8gLySxXtyI@celegans.imp.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_453DCC989E0E42B39FC71018FCACF8BAfuberlinde_" MIME-Version: 1.0 Date: Mon, 25 Nov 2019 11:19:45 +0100 X-Original-Date: Mon, 25 Nov 2019 10:19:45 +0000 X-Originating-IP: 130.133.170.207 X-Original-X-Originating-IP: [130.133.175.151] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574677188-0002BF59-50D0416B/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,HTML_MESSAGE, T_FILL_THIS_FORM_SHORT 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inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBau-000y3c-1I>; Mon, 25 Nov 2019 11:27:48 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.38.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) with esmtpsa (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1iZBat-003vCn-P7>; Mon, 25 Nov 2019 11:27:47 +0100 From: Hannes Hauswedell To: Jin Li Cc: SeqAn Development Date: Mon, 25 Nov 2019 11:27:48 +0100 Message-ID: <1896257.4WAli8B44Z@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: 160.45.38.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574677668-0002BF59-9E88269F/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 X-Spam-Checker-Version: SpamAssassin 3.4.2 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] The definition of classes in SeqAn2. 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: Mon, 25 Nov 2019 10:27:48 -0000 Am Samstag, 23. November 2019, 23:08:48 CET schrieb Jin Li: > Hi all, >=20 > I am trying to adapt SeqAn2 in my program. I have a problem to find > out class definitions in SeqAn2. For example, in the following > tutorial, > https://seqan.readthedocs.io/en/master/Tutorial/InputOutput/SamAndBamIO.h= tml > #accessing-the-header >=20 > `TBamContext` is used to define a variable for header information, and > I want to extract the reference names (such as chr1, chr2, xxx) from > it, and save them as std::string in native C++. However, the class's > definition is not clear, and the interfaces for the conversion are not > directly available either. Can you help point out documentation about > these class type definitions in SeqAn2? Thank you. TBamContext is defined just in the line above where it is used. In general = all=20 class names that are in the form TFooBar are either template parameters or = are=20 local aliases (typedefs) for longer typenames that are tedious to write=20 everytime. In the example mentioned by you, TBamContext is defined as =46ormattedFileContext::Type which is a "metafunction" that returns the context-type from BamFileIn whic= h=20 is typically BamIOContext. Best regards, =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 From Rene.Rahn@fu-berlin.de Mon Nov 25 15:19:11 2019 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 <1iZFCn-0025KZ-F3>; Mon, 25 Nov 2019 15:19:10 +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 <1iZFCn-0032Y5-C4>; Mon, 25 Nov 2019 15:19:09 +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 <1iZFCn-000ZYA-0q>; Mon, 25 Nov 2019 15:19:09 +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; Mon, 25 Nov 2019 15:19:07 +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; Mon, 25 Nov 2019 15:19:07 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Home brew installation error message Thread-Index: AQHVngHem8SiPj7cx0aC/HNCmAtdkaeQx0QAgAsijYA= Message-ID: <1FDAC402-8B38-442B-860F-A35290004564@fu-berlin.de> References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> <1723D540-DB75-45AE-A87B-950B8ACB3D32@me.com> In-Reply-To: <1723D540-DB75-45AE-A87B-950B8ACB3D32@me.com> 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mr85p00im-zteg06021601.me.com (Postfix) with ESMTPSA id 2155E400842 for ; Mon, 25 Nov 2019 14:38:54 +0000 (UTC) From: =?utf-8?Q?Werner_M=C3=BCller?= Content-Type: multipart/alternative; boundary="Apple-Mail=_DC185E66-7505-4EBA-97BC-3B09822C9EFE" Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Date: Mon, 25 Nov 2019 14:38:52 +0000 References: <43CA7521-1CC4-4039-B3B9-48FE0248113F@me.com> <1723D540-DB75-45AE-A87B-950B8ACB3D32@me.com> <1FDAC402-8B38-442B-860F-A35290004564@fu-berlin.de> To: SeqAn Development In-Reply-To: <1FDAC402-8B38-442B-860F-A35290004564@fu-berlin.de> Message-Id: X-Mailer: Apple Mail (2.3445.104.11) X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10434:, , definitions=2019-11-25_03:, , signatures=0 X-Proofpoint-Spam-Details: rule=notspam policy=default score=0 suspectscore=0 malwarescore=0 phishscore=0 bulkscore=0 spamscore=0 clxscore=1015 mlxscore=0 mlxlogscore=999 adultscore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.0.1-1908290000 definitions=main-1911250133 X-Originating-IP: 17.58.23.187 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1574692738-0002BF59-3078256B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, 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,DKIM_VALID_EF,FREEMAIL_ENVFROM_END_DIGIT,FREEMAIL_FROM, HTML_MESSAGE,SPF_HELO_NONE,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.2 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Home brew installation error message 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: Mon, 25 Nov 2019 14:39:02 -0000 --Apple-Mail=_DC185E66-7505-4EBA-97BC-3B09822C9EFE Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Installation works, Thanks for implementing the change. Yours Werner M=C3=BCller > On 25 Nov 2019, at 14:19, Rahn, Ren=C3=A9 = wrote: >=20 > Hi,=20 >=20 > so homebrew/science was deprecated a while ago. > SeqAn 2.4.0 is available through the tap brewsci/bio = . >=20 > So,=20 >=20 > brew tap brewsci/bio > brew install seqan >=20 > should already work. Can you test that this resolves the issue? >=20 > Best regards, >=20 > The SeqAn Team >=20 >> On 18. Nov 2019, at 13:16, Werner M=C3=BCller > wrote: >>=20 >> May be best would be to use brewsci/bio ? >>=20 >>=20 >> ----- >>=20 >> Here is the information from the homebrew page: >> Homebrew/science (deprecated) >>=20 >> These formulae provided software tailored to scientific endeavours. >>=20 >> This tap was deprecated because it had different goals from the wider = Homebrew organisation (e.g. Linuxbrew CI/support). All widely used, = buildable formulae were migrated to homebrew/core. >>=20 >> If you wish to migrate other widely used formulae = to = Homebrew/homebrew-core please submit a pull request = there. >>=20 >> You may be interested in the brewsci/bio = and brewsci/science = taps. >>=20 >>> On 18 Nov 2019, at 12:17, Werner M=C3=BCller > wrote: >>>=20 >>> homebrew/science was deprecated. This tap is now empty as all its = formulae were migrated. >>>=20 >>> Most likely you need to move it to a new directory. >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev = >>=20 >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 > --- >=20 > Ren=C3=A9 Rahn > Ph.D. Student (de.NBI - CIBI) > -------------------------------- > Tel: (+49) 30 838 72974 > Mail: rene.rahn@fu-berlin.de > -------------------------------- > Institute of Computer Science > Algorithmic Bioinformatics (ABI) > -------------------------------- > Freie Universit=C3=A4t Berlin > Takustra=C3=9Fe 9 > 14195 Berlin > -------------------------------- >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_DC185E66-7505-4EBA-97BC-3B09822C9EFE Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Installation works,
Thanks for implementing = the change.

Yours
Werner M=C3=BCller

On 25 Nov 2019, at 14:19, Rahn, Ren=C3=A9 <Rene.Rahn@fu-berlin.de> wrote:

Hi, 

so homebrew/science was deprecated a while ago.
SeqAn 2.4.0 is available through the tap brewsci/bio.

So, 

brew tap brewsci/bio
brew install seqan

should already work. Can =
you test that this resolves the issue?

Best regards,

The SeqAn Team

On 18. Nov 2019, at 13:16, Werner M=C3=BCller <wmueller4711@me.com>= wrote:

May be best would be to use brewsci/bio ?


-----

Here is the information from the homebrew page:

Homebrew/science (deprecated)

These formulae provided software tailored to scientific = endeavours.

This tap was deprecated because it had different goals from the wider = Homebrew organisation (e.g. Linuxbrew CI/support). All widely used, = buildable formulae were migrated to homebrew/core.

If you wish to migrate other widely used = formulae to Homebrew/homebrew-core please submit a pull request there.

You may be interested in the brewsci/bio and brewsci/science taps.

On 18 Nov 2019, at 12:17, Werner M=C3=BCller <wmueller4711@me.com>= wrote:

homebrew/science was deprecated. This tap is now empty as all = its formulae were migrated.
Most likely you need to move it to a new = directory.
_______________________________________________
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

---

Ren=C3=A9 Rahn
Ph.D. Student (de.NBI - CIBI)
--------------------------------
Tel:  (+49) = 30 838 72974
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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