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[76.167.196.136]) by mx.google.com with ESMTPSA id se3sm6579348pbc.24.2015.01.09.01.51.51 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Fri, 09 Jan 2015 01:51:52 -0800 (PST) From: Jordan Willis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Message-Id: Date: Fri, 9 Jan 2015 02:00:09 -0800 To: seqan-dev@lists.fu-berlin.de Mime-Version: 1.0 (Mac OS X Mail 7.3 \(1878.6\)) X-Mailer: Apple Mail (2.1878.6) X-Originating-IP: 209.85.220.41 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1420797116-0000127A-EFE4F3FC/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500122, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.8 required=5.0 tests=FREEMAIL_FROM, FU_BOGO_UNSURE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL, T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Container type for storing sequences in memory 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, 09 Jan 2015 09:51:58 -0000 Hi, I was wondering if there is a builtin container in Seqan for storing a = small database of sequence ids and sequences that can be stored in = memory. The sequences will be continually iterated through and local = alignments will be performed. Does anyone have any recommendations for = this or perhaps point me to one of the builtin apps that does this? Thanks so much, j= From bnbowman@gmail.com Sat Jan 10 03:16:26 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Y9lbE-002H3Q-Bj>; Sat, 10 Jan 2015 03:16:24 +0100 Received: from mail-yh0-f53.google.com ([209.85.213.53]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Y9lbE-002vl9-1x>; Sat, 10 Jan 2015 03:16:24 +0100 Received: by mail-yh0-f53.google.com with SMTP id i57so5693715yha.12 for ; Fri, 09 Jan 2015 18:16:21 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=3mdRAxaikOa0t59iAiqYsD1rJsQ53bee2TA7QRTv4gs=; b=sQzGwS3nD40lMllV88jQmkk8tRhNRQcHWlRfN6vTjzCLQRouwlf6R5EYUMe0JsN8Uf uJkfnqt0YWgBdx6iLwT29ITqZudCoh4NX8PvZRWhsXVqZONYzzs39XPWNc8MLkwCTmCK +GxDGxPcPwoPlxxl4xu23rL5voHHDlyOl4adNTt6vSklDvnCdnjTTVwksvoyX+pU8iU8 P0MIqCOFWbN6GHBL8cPCP9UY7PNtrCEVl7zDptJODs915lW7q2c5NZidzq0EgoXu2CP0 81VzUKRYYyAVeReID6DMi24+879Fl06uPJg2JJeasjGCJ8DMC/JbgD2zpDtlZwuu9wT3 Tz3Q== MIME-Version: 1.0 X-Received: by 10.236.63.6 with SMTP id z6mr13870377yhc.65.1420856181135; Fri, 09 Jan 2015 18:16:21 -0800 (PST) Received: by 10.170.86.86 with HTTP; Fri, 9 Jan 2015 18:16:21 -0800 (PST) In-Reply-To: References: Date: Fri, 9 Jan 2015 18:16:21 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=089e01294ff0f42150050c42dbdc X-Originating-IP: 209.85.213.53 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1420856184-0000127A-54E28B28/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.038353, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Two Alignment Questions 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: Sat, 10 Jan 2015 02:16:26 -0000 --089e01294ff0f42150050c42dbdc Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Rene, >What do you mean by accuracy? What do you need exactly? What I am trying to do is write a tool to align single-molecule sequencing data (PacBio, Oxford Nanopore) to reference genomes. For which the alignment accuracy and the break-down of the types of errors is very useful, as the per-read quality on both platforms varies substantially. What I'd like are member methods or functions-on-alignment-objects to give the following: -The number of base-pair matches in the alignment -The number of mismatches in the alignment -The number of insertions in the alignment -The number of deletions in the alignment -The alignment string as represented by the Align object's toString() metho= d The first four I need to summarize the similarity of an alignment (i.e. indels are likely sequencing error, where as mismatches are likely not), while the latter is helpful in creating alternate representations for alignments Does that help? -B On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9 wrote: > Hey Brett, > > > On 30 Dec 2014, at 21:29, Brett Bowman wrote: > > 1) Is there an easy way to get the accuracy of an Alignment object, or > is that something I need to calculate myself? > > > What do you mean by accuracy? What do you need exactly? > The Align data structure simply represents the computed alignment. The > score is returned by the global align interface. > There are several ways to manipulate the alignment of gaps and to compute > all best traceback paths. However, those options are not supported on the > high level interfaces but only in the core of the alignment engine. > If you tell me what you need exactly we can think of a way to make those > interfaces public which is planned for the future anyway. > But there is no method telling you the accuracy of the =E2=80=9Ccomputed" > alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Please, g= ive me some > specifics and we see if we can incorporate this. > ... > Well, there is a method in the tool seqan-tcoffee, which checks if the > computed alignment is correct given the score model and the alignment, bu= t > I believe this is not what you are looking for? > > > 2) bandedChainAlignment fails messily when given a Vector of Seeds > instead of a String, where as other functions work fine (e.g. > chainSeedsGlobally). Why does it work for the one and not the other? > Excerpt from error message below. > > """ > /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: > call to 'end' is ambiguous > SEQAN_ASSERT(itEnd !=3D static_cast(end(seedSet))); > ^~~ > /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded from > macro 'SEQAN_ASSERT' > (_arg1), # _arg1)) { = \ > ^ > /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: i= n > instantiation of function template specialization > > ... > > /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in > instantiation of function template specialization > > 'seqan::bandedChainAlignment seqan::Dna5_>, seqan::Alloc >, seqan::Tag, > std::vector, > seqan::DefaultSeedConfig>, > std::allocator, > seqan::DefaultSeedConfig> > >, long, > seqan::Tag, seqan::Tag, false, > false, false, false, seqan::Tag >' requested here > return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, > alignConfig, bandExtension); > ^ > /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in > instantiation of function template specialization > > 'seqan::bandedChainAlignment seqan::Dna5_>, seqan::Alloc >, seqan::Tag, > std::vector, > seqan::DefaultSeedConfig>, > std::allocator, > seqan::DefaultSeedConfig> > >, long, > seqan::Tag, false, false, false, false, > seqan::Tag >' requested here > long alnScore =3D bandedChainAlignment(alignment, *seedChain, > scoring, globalConfig); > ^ > /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation of > function template specialization > 'RefChainsToAlignments seqan::Tag > ()>' requested here > auto alignments =3D RefChainsToAlignments(record->Seq, > ^ > /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: > candidate template ignored: substitution failure [with TSeedSet =3D > std::vector, > seqan::DefaultSeedConfig>, > std::allocator, > seqan::DefaultSeedConfig> > >] > _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) > "=E2=80=9D" > > > Ok, this seems to be a bug to me. > I=E2=80=99ll have a look into it. > > > Sincerely, > -Brett > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > > Bests, > > Ren=C3=A9 > > --- > > Ren=C3=A9 Rahn > Ph.D. Student > -------------------------------- > Tel: (+49) 30 838 75277 > 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 > > --089e01294ff0f42150050c42dbdc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks Rene,

>What do you= mean by accuracy? What do you need exactly?=C2=A0

What I am trying to do i= s write a tool to align single-molecule sequencing data (PacBio, Oxford Nan= opore) to reference genomes.=C2=A0 For which the alignment accuracy and the= break-down of the types of errors is very useful, as the per-read quality = on both platforms varies substantially.
=
What I'd like are member method= s or functions-on-alignment-objects to give the following:
-The number of base-pair matches in the alignment
=
-The number of mismatches in the alignment
-The number of insertions in the alignment=
-The number of deletions in the alignme= nt
-The alignment string as represented = by the Align object's toString() method

The first four I need to summar= ize the similarity of an alignment (i.e. indels are likely sequencing error= , where as mismatches are likely not), while the latter is helpful in creat= ing alternate representations for alignments

Does that help?

-B

On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9 <<= a href=3D"mailto:rene.maerker@fu-berlin.de" target=3D"_blank">rene.maerker@= fu-berlin.de> wrote:
Hey Brett,=C2=A0


On 30 Dec 2014, at 21:29, Brett Bowman <bnbowman@gmail.com> wrote:

1) =C2=A0Is there an easy way to get the accuracy of an Alignment obje= ct, or is that something I need to calculate myself?

What do you mean by accuracy? What do you need exactly?=C2=A0
The Align data structure simply represents the computed alignment. The= score is returned by the global align interface.=C2=A0
There are several ways to manipulate the alignment of gaps and to comp= ute all best traceback paths. However, those options are not supported on t= he high level interfaces but only in the core of the alignment engine.=C2= =A0
If you tell me what you need exactly we can think of a way to make tho= se interfaces public which is planned for the future anyway.
But there is no method telling you the accuracy of the =E2=80=9Ccomput= ed" alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Pl= ease, give me some specifics and we see if we can incorporate this.
...
Well, there is a method in the tool seqan-tcoffee, which checks if the= computed alignment is correct given the score model and the alignment, but= I believe this is not what you are looking for?


2) =C2=A0bandedChainAlignment fails messily when given a Vector of See= ds instead of a String, where as other functions work fine (e.g. chainSeeds= Globally).=C2=A0 Why does it work for the one and not the other?=C2=A0 Exce= rpt from error message below.

"""
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error:= call to 'end' is ambiguous
=C2=A0 =C2=A0 SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator&= gt;(end(seedSet)));
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded f= rom macro 'SEQAN_ASSERT'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 (_arg1), # _arg1)) { =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 \
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0^
/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note= : in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in ins= tantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, seqan::Tag<s= eqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default= _> >' requested here
=C2=A0 =C2=A0 return bandedChainAlignment(align, seedSet, scoreScheme,= scoreScheme, alignConfig, bandExtension);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^
/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in i= nstantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, false, false, f= alse, false, seqan::Tag<seqan::Default_> >' requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 long alnScore =3D bandedChainAlignment(ali= gnment, *seedChain, scoring, globalConfig);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation= of function template specialization 'RefChainsToAlignments<seqan::A= lignConfig<false, true, true, false,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Default_> > ()>'= ; requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 auto alignments =3D RefChainsToAlignments(= record->Seq,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 ^
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: ca= ndidate template ignored: substitution failure [with TSeedSet =3D std::vect= or<seqan::Seed<seqan::Tag<seqan::Simple_>,
=C2=A0 =C2=A0 =C2=A0 seqan::DefaultSeedConfig>, std::allocator<s= eqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>= ; > >]
_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
"=E2=80=9D"=C2=A0

Ok, this seems to be a bug to me.
I=E2=80=99ll have a look into it.


Sincerely,
-Brett
_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

Bests,=C2=A0

Ren=C3=A9=C2=A0

---

Ren=C3=A9 Rahn
Ph.D. Student
--------------------------------
--------------------------------
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.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


--089e01294ff0f42150050c42dbdc-- From manuel.holtgrewe@fu-berlin.de Sat Jan 10 11:21:15 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Y9tAO-002yMp-VP>; Sat, 10 Jan 2015 11:21:13 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Y9tAO-0009C3-Tt>; Sat, 10 Jan 2015 11:21:12 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Y9tAO-0039Vr-K6>; Sat, 10 Jan 2015 11:21:12 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0210.002; Sat, 10 Jan 2015 11:21:11 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Two Alignment Questions Thread-Index: AQHQJG9gO46vv1/ke0ClYCoJhXa1OJy3eUiAgAEj74CAAJgwyw== Message-ID: References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B962864F0ex02acampusfube_" MIME-Version: 1.0 Date: Sat, 10 Jan 2015 11:21:10 +0100 X-Original-Date: Sat, 10 Jan 2015 10:21:10 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1420885272-0000127A-7FD87333/0/0 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 X-Spam-Checker-Version: SpamAssassin 3.4.0 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Two Alignment Questions 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: Sat, 10 Jan 2015 10:21:15 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B962864F0ex02acampusfube_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Does this help? http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStatshttp://docs.se= qan.de/seqan/develop/?p=3DcomputeAlignmentStats *m ________________________________ From: Brett Bowman [bnbowman@gmail.com] Sent: Saturday, January 10, 2015 3:16 AM To: SeqAn Development Subject: Re: [Seqan-dev] Two Alignment Questions Thanks Rene, >What do you mean by accuracy? What do you need exactly? What I am trying to do is write a tool to align single-molecule sequencing = data (PacBio, Oxford Nanopore) to reference genomes. For which the alignme= nt accuracy and the break-down of the types of errors is very useful, as th= e per-read quality on both platforms varies substantially. What I'd like are member methods or functions-on-alignment-objects to give = the following: -The number of base-pair matches in the alignment -The number of mismatches in the alignment -The number of insertions in the alignment -The number of deletions in the alignment -The alignment string as represented by the Align object's toString() metho= d The first four I need to summarize the similarity of an alignment (i.e. ind= els are likely sequencing error, where as mismatches are likely not), while= the latter is helpful in creating alternate representations for alignments Does that help? -B On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=E9 > wrote: Hey Brett, On 30 Dec 2014, at 21:29, Brett Bowman > wrote: 1) Is there an easy way to get the accuracy of an Alignment object, or is = that something I need to calculate myself? What do you mean by accuracy? What do you need exactly? The Align data structure simply represents the computed alignment. The scor= e is returned by the global align interface. There are several ways to manipulate the alignment of gaps and to compute a= ll best traceback paths. However, those options are not supported on the hi= gh level interfaces but only in the core of the alignment engine. If you tell me what you need exactly we can think of a way to make those in= terfaces public which is planned for the future anyway. But there is no method telling you the accuracy of the =93computed" alignme= nt compared to another =93real=94 alignment. Please, give me some specifics= and we see if we can incorporate this. ... Well, there is a method in the tool seqan-tcoffee, which checks if the comp= uted alignment is correct given the score model and the alignment, but I be= lieve this is not what you are looking for? 2) bandedChainAlignment fails messily when given a Vector of Seeds instead= of a String, where as other functions work fine (e.g. chainSeedsGlobally).= Why does it work for the one and not the other? Excerpt from error messa= ge below. """ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: call= to 'end' is ambiguous SEQAN_ASSERT(itEnd !=3D static_cast(end(seedSet))); ^~~ /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded from m= acro 'SEQAN_ASSERT' (_arg1), # _arg1)) { \ ^ /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: in = instantiation of function template specialization ... /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in instanti= ation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSee= dConfig>, std::allocator, seqan::Def= aultSeedConfig> > >, long, seqan::Tag, seqan::Tag, false, false,= false, false, seqan::Tag >' requested here return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, a= lignConfig, bandExtension); ^ /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in instan= tiation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSee= dConfig>, std::allocator, seqan::Def= aultSeedConfig> > >, long, seqan::Tag, false, false, false, false, seqan::Tag >' requested here long alnScore =3D bandedChainAlignment(alignment, *seedChain, scori= ng, globalConfig); ^ /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation of f= unction template specialization 'RefChainsToAlignments > ()>' requested here auto alignments =3D RefChainsToAlignments(record->Seq, ^ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: candida= te template ignored: substitution failure [with TSeedSet =3D std::vector, seqan::DefaultSeedConfig>, std::allocator, seqan::DefaultSeedConfig> > >] _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) "=94" Ok, this seems to be a bug to me. I=92ll have a look into it. Sincerely, -Brett _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev Bests, Ren=E9 --- Ren=E9 Rahn Ph.D. Student -------------------------------- Tel: (+49) 30 838 75277 Mail: rene.rahn@fu-berlin.de -------------------------------- Institute of Computer Science Algorithmic Bioinformatics (ABI) -------------------------------- Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin -------------------------------- _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_FCCAB9D80C3DAB47B5601C5B0E62872B962864F0ex02acampusfube_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Does this help?

http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStatshttp://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStats

*m

From: Brett Bowman [bnbowman@gmail.com] Sent: Saturday, January 10, 2015 3:16 AM
To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Thanks Rene,

>What do you mean by accuracy? What do you= need exactly? 

What I am trying to do is write a tool to ali= gn single-molecule sequencing data (PacBio, Oxford Nanopore) to reference g= enomes.  For which the alignment accuracy and the break-down of the ty= pes of errors is very useful, as the per-read quality on both platforms varies substantially.

What I'd like are member methods or functions= -on-alignment-objects to give the following:
-The number of base-pair matches in the align= ment
-The number of mismatches in the alignment
-The number of insertions in the alignment
-The number of deletions in the alignment
-The alignment string as represented by the A= lign object's toString() method

The first four I need to summarize the simila= rity of an alignment (i.e. indels are likely sequencing error, where as mis= matches are likely not), while the latter is helpful in creating alternate = representations for alignments

Does that help?

-B

On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=E9 <rene.mae= rker@fu-berlin.de> wrote:
Hey Brett, 



1)  Is there an easy way to get the accuracy of an Alignment obje= ct, or is that something I need to calculate myself?

What do you mean by accuracy? What do you need exactly? 
The Align data structure simply represents the computed alignment. The= score is returned by the global align interface. 
There are several ways to manipulate the alignment of gaps and to comp= ute all best traceback paths. However, those options are not supported on t= he high level interfaces but only in the core of the alignment engine. = ;
If you tell me what you need exactly we can think of a way to make tho= se interfaces public which is planned for the future anyway.
But there is no method telling you the accuracy of the =93computed&quo= t; alignment compared to another =93real=94 alignment. Please, give me some= specifics and we see if we can incorporate this.
...
Well, there is a method in the tool seqan-tcoffee, which checks if the= computed alignment is correct given the score model and the alignment, but= I believe this is not what you are looking for?


2)  bandedChainAlignment fails messily when given a Vector of See= ds instead of a String, where as other functions work fine (e.g. chainSeeds= Globally).  Why does it work for the one and not the other?  Exce= rpt from error message below.

"""
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error:= call to 'end' is ambiguous
    SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator&= gt;(end(seedSet)));
                    =                      = ;               ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded f= rom macro 'SEQAN_ASSERT'
                    =                      = ; (_arg1), # _arg1)) {           \
                    =                      = ;  ^
/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note= : in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in ins= tantiation of function template specialization
      'seqan::bandedChainAlignment<seqan::String<= seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void&= gt; >, seqan::Tag<seqan::ArrayGaps_>,
      std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
      seqan::Tag<seqan::Simple_>, seqan::Tag<s= eqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default= _> >' requested here
    return bandedChainAlignment(align, seedSet, scoreScheme,= scoreScheme, alignConfig, bandExtension);
           ^
/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: no= te: in instantiation of function template specialization
      'seqan::bandedChainAlignment<seqan::String<= seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void&= gt; >, seqan::Tag<seqan::ArrayGaps_>,
      std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
      seqan::Tag<seqan::Simple_>, false, false, f= alse, false, seqan::Tag<seqan::Default_> >' requested here
        long alnScore =3D bandedChainAlignment(ali= gnment, *seedChain, scoring, globalConfig);
                    =     ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in insta= ntiation of function template specialization 'RefChainsToAlignments<seqa= n::AlignConfig<false, true, true, false,
      seqan::Tag<seqan::Default_> > ()>' re= quested here
        auto alignments =3D RefChainsToAlignments(= record->Seq,
                    =       ^
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: ca= ndidate template ignored: substitution failure [with TSeedSet =3D std::vect= or<seqan::Seed<seqan::Tag<seqan::Simple_>,
      seqan::DefaultSeedConfig>, std::allocator<s= eqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>= ; > >]
_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
"=94" 

Ok, this seems to be a bug to me.
I=92ll have a look into it.


Sincerely,
-Brett
_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

Bests, 

Ren=E9 

---

Ren=E9 Rahn
Ph.D. Student
--------------------------------
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=E4t Berlin
Takustra=DFe 9
14195 Berlin
--------------------------------


_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev


--_000_FCCAB9D80C3DAB47B5601C5B0E62872B962864F0ex02acampusfube_-- From bnbowman@gmail.com Sun Jan 11 18:47:57 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YAMcE-000vVU-Uc>; Sun, 11 Jan 2015 18:47:55 +0100 Received: from mail-yk0-f175.google.com ([209.85.160.175]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YAMcE-002qNN-Ka>; Sun, 11 Jan 2015 18:47:54 +0100 Received: by mail-yk0-f175.google.com with SMTP id 200so7692931ykr.6 for ; Sun, 11 Jan 2015 09:47:52 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=zOoXSQmhXt0kocrNiUZ++TiflYQUiOcjyj3p8WKjR38=; b=aNFL9mL+q7ZTa5xJS/hQQGi7/VnWRa4d2Sp9Biix9snWdyecoWiq7xU0rTGmJKo0zL cuaJJkmFESrUxHAKYIB2Rx/BaWVN846vJIn1R4YO1GnHWFWaJ6pFARuhsLRzgRbffBY2 R4Jvs7SE165NaUwOHByTS8+AtSrtsnNkC36RHjzCK1v0rU8dytaO564RwaIhgs/I4u/Y E8GWGDNolqNrx8QmzW/oG4hgHLsdnLwDnfTC8A8pjh9iiJ1MouJug32M6XpnUwZH0VhX rDVcCQ7L5rYpFCvk3cDXhs6etNn7K9D/d236DQttmpnoCA7uYoRZDHkIXmktyMG4VjLS zlDg== MIME-Version: 1.0 X-Received: by 10.170.147.130 with SMTP id o124mr22103629ykc.101.1420998472034; Sun, 11 Jan 2015 09:47:52 -0800 (PST) Received: by 10.170.86.86 with HTTP; Sun, 11 Jan 2015 09:47:51 -0800 (PST) In-Reply-To: References: Date: Sun, 11 Jan 2015 09:47:51 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a1139239a26f194050c63fd77 X-Originating-IP: 209.85.160.175 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1420998474-0000127A-F4B88FCD/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.084309, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Two Alignment Questions 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: Sun, 11 Jan 2015 17:47:57 -0000 --001a1139239a26f194050c63fd77 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Manuel, I saw the AlignmentStats class when I was digging around in the API for what I need, but I'm afraid it doesn't quite fit: -It doesn't differentiate between Insertions and Deletions (the ratio of which is important for diagnosing some sequencing problems and bad alignments) -It doesn't appear to provide access to the alignment string, meaning I still need to traverse the whole alignment to generate alternate representations. -B On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manuel < manuel.holtgrewe@fu-berlin.de> wrote: > Does this help? > > http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStats > http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStats > > *m > > ------------------------------ > *From:* Brett Bowman [bnbowman@gmail.com] > *Sent:* Saturday, January 10, 2015 3:16 AM > *To:* SeqAn Development > *Subject:* Re: [Seqan-dev] Two Alignment Questions > > Thanks Rene, > > >What do you mean by accuracy? What do you need exactly? > > What I am trying to do is write a tool to align single-molecule > sequencing data (PacBio, Oxford Nanopore) to reference genomes. For whic= h > the alignment accuracy and the break-down of the types of errors is very > useful, as the per-read quality on both platforms varies substantially. > > What I'd like are member methods or functions-on-alignment-objects to > give the following: > -The number of base-pair matches in the alignment > -The number of mismatches in the alignment > -The number of insertions in the alignment > -The number of deletions in the alignment > -The alignment string as represented by the Align object's toString() > method > > The first four I need to summarize the similarity of an alignment (i.e. > indels are likely sequencing error, where as mismatches are likely not), > while the latter is helpful in creating alternate representations for > alignments > > Does that help? > > -B > > On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9 > wrote: > >> Hey Brett, >> >> >> On 30 Dec 2014, at 21:29, Brett Bowman wrote: >> >> 1) Is there an easy way to get the accuracy of an Alignment object, or >> is that something I need to calculate myself? >> >> >> What do you mean by accuracy? What do you need exactly? >> The Align data structure simply represents the computed alignment. The >> score is returned by the global align interface. >> There are several ways to manipulate the alignment of gaps and to comput= e >> all best traceback paths. However, those options are not supported on th= e >> high level interfaces but only in the core of the alignment engine. >> If you tell me what you need exactly we can think of a way to make those >> interfaces public which is planned for the future anyway. >> But there is no method telling you the accuracy of the =E2=80=9Ccomputed= " >> alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Please, = give me some >> specifics and we see if we can incorporate this. >> ... >> Well, there is a method in the tool seqan-tcoffee, which checks if the >> computed alignment is correct given the score model and the alignment, b= ut >> I believe this is not what you are looking for? >> >> >> 2) bandedChainAlignment fails messily when given a Vector of Seeds >> instead of a String, where as other functions work fine (e.g. >> chainSeedsGlobally). Why does it work for the one and not the other? >> Excerpt from error message below. >> >> """ >> /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: >> call to 'end' is ambiguous >> SEQAN_ASSERT(itEnd !=3D static_cast(end(seedSet)))= ; >> ^~~ >> /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded fro= m >> macro 'SEQAN_ASSERT' >> (_arg1), # _arg1)) { = \ >> ^ >> /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: >> in instantiation of function template specialization >> >> ... >> >> /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in >> instantiation of function template specialization >> >> 'seqan::bandedChainAlignment> seqan::Dna5_>, seqan::Alloc >, seqan::Tag, >> std::vector, >> seqan::DefaultSeedConfig>, >> std::allocator, >> seqan::DefaultSeedConfig> > >, long, >> seqan::Tag, seqan::Tag, false, >> false, false, false, seqan::Tag >' requested here >> return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme= , >> alignConfig, bandExtension); >> ^ >> /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in >> instantiation of function template specialization >> >> 'seqan::bandedChainAlignment> seqan::Dna5_>, seqan::Alloc >, seqan::Tag, >> std::vector, >> seqan::DefaultSeedConfig>, >> std::allocator, >> seqan::DefaultSeedConfig> > >, long, >> seqan::Tag, false, false, false, false, >> seqan::Tag >' requested here >> long alnScore =3D bandedChainAlignment(alignment, *seedChain, >> scoring, globalConfig); >> ^ >> /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation o= f >> function template specialization >> 'RefChainsToAlignments> seqan::Tag > ()>' requested here >> auto alignments =3D RefChainsToAlignments(record->Seq, >> ^ >> /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: >> candidate template ignored: substitution failure [with TSeedSet =3D >> std::vector, >> seqan::DefaultSeedConfig>, >> std::allocator, >> seqan::DefaultSeedConfig> > >] >> _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) >> "=E2=80=9D" >> >> >> Ok, this seems to be a bug to me. >> I=E2=80=99ll have a look into it. >> >> >> Sincerely, >> -Brett >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> >> Bests, >> >> Ren=C3=A9 >> >> --- >> >> Ren=C3=A9 Rahn >> Ph.D. Student >> -------------------------------- >> Tel: (+49) 30 838 75277 >> 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 >> >> > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > --001a1139239a26f194050c63fd77 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Manuel,

I saw the AlignmentStats class = when I was digging around in the API for what I need, but I'm afraid it= doesn't quite fit:
-It doesn't differentiate between Ins= ertions and Deletions (the ratio of which is important for diagnosing some = sequencing problems and bad alignments)
-It doesn't appear to= provide access to the alignment string, meaning I still need to traverse t= he whole alignment to generate alternate representations.

-B

On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manuel &= lt;manue= l.holtgrewe@fu-berlin.de> wrote:
Does this help?


*m

Fro= m: Brett Bowman [bnbowman@gmail.com]
Sent: Saturday, January 10, 2015 3:16 AM
To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Thanks Rene,

>What do you mean by accuracy? What do you= need exactly?=C2=A0

What I am trying to do is write a tool to ali= gn single-molecule sequencing data (PacBio, Oxford Nanopore) to reference g= enomes.=C2=A0 For which the alignment accuracy and the break-down of the ty= pes of errors is very useful, as the per-read quality on both platforms varies substantially.

What I'd like are member methods or funct= ions-on-alignment-objects to give the following:
-The number of base-pair matches in the align= ment
-The number of mismatches in the alignment
-The number of insertions in the alignment
-The number of deletions in the alignment
-The alignment string as represented by the A= lign object's toString() method

The first four I need to summarize the simila= rity of an alignment (i.e. indels are likely sequencing error, where as mis= matches are likely not), while the latter is helpful in creating alternate = representations for alignments

Does that help?

-B

On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9= <rene.mae= rker@fu-berlin.de> wrote:
Hey Brett,=C2=A0


On 30 Dec 2014, at 21:29, Brett Bowman <bnbowman@gmail.com> wrote:

1) =C2=A0Is there an easy way to get the accuracy of an Alignment obje= ct, or is that something I need to calculate myself?
What do you mean by accuracy? What do you need exactly?=C2=A0
The Align data structure simply represents the computed alignment. The= score is returned by the global align interface.=C2=A0
There are several ways to manipulate the alignment of gaps and to comp= ute all best traceback paths. However, those options are not supported on t= he high level interfaces but only in the core of the alignment engine.=C2= =A0
If you tell me what you need exactly we can think of a way to make tho= se interfaces public which is planned for the future anyway.
But there is no method telling you the accuracy of the =E2=80=9Ccomput= ed" alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Pl= ease, give me some specifics and we see if we can incorporate this.
...
Well, there is a method in the tool seqan-tcoffee, which checks if the= computed alignment is correct given the score model and the alignment, but= I believe this is not what you are looking for?


2) =C2=A0bandedChainAlignment fails messily when given a Vector of See= ds instead of a String, where as other functions work fine (e.g. chainSeeds= Globally).=C2=A0 Why does it work for the one and not the other?=C2=A0 Exce= rpt from error message below.

"""
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error:= call to 'end' is ambiguous
=C2=A0 =C2=A0 SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator&= gt;(end(seedSet)));
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded f= rom macro 'SEQAN_ASSERT'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 (_arg1), # _arg1)) { =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 \
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0^
/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note= : in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in ins= tantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, seqan::Tag<s= eqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default= _> >' requested here
=C2=A0 =C2=A0 return bandedChainAlignment(align, seedSet, scoreScheme,= scoreScheme, alignConfig, bandExtension);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^
/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in i= nstantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, false, false, f= alse, false, seqan::Tag<seqan::Default_> >' requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 long alnScore =3D bandedChainAlignment(ali= gnment, *seedChain, scoring, globalConfig);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation= of function template specialization 'RefChainsToAlignments<seqan::A= lignConfig<false, true, true, false,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Default_> > ()>'= ; requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 auto alignments =3D RefChainsToAlignments(= record->Seq,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 ^
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: ca= ndidate template ignored: substitution failure [with TSeedSet =3D std::vect= or<seqan::Seed<seqan::Tag<seqan::Simple_>,
=C2=A0 =C2=A0 =C2=A0 seqan::DefaultSeedConfig>, std::allocator<s= eqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>= ; > >]
_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
"=E2=80=9D"=C2=A0

Ok, this seems to be a bug to me.
I=E2=80=99ll have a look into it.


Sincerely,
-Brett
_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

Bests,=C2=A0

Ren=C3=A9=C2=A0

---

Ren=C3=A9 Rahn
Ph.D. Student
--------------------------------
--------------------------------
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



_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


--001a1139239a26f194050c63fd77-- From manuel.holtgrewe@fu-berlin.de Mon Jan 12 10:11:29 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YAb1z-001p0M-5b>; Mon, 12 Jan 2015 10:11:27 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YAb1z-002KDq-43>; Mon, 12 Jan 2015 10:11:27 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YAb1y-002X8F-QQ>; Mon, 12 Jan 2015 10:11:27 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0210.002; Mon, 12 Jan 2015 10:11:25 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Two Alignment Questions Thread-Index: AQHQJG9gO46vv1/ke0ClYCoJhXa1OJy3eUiAgAEj74CAAJgwy4AB/meAgAESi04= Message-ID: References: , In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B962867DBex02acampusfube_" MIME-Version: 1.0 Date: Mon, 12 Jan 2015 10:11:24 +0100 X-Original-Date: Mon, 12 Jan 2015 09:11:24 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1421053887-0000127A-A2F7348A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000024, 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 3.4.0 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Two Alignment Questions 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, 12 Jan 2015 09:11:29 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B962867DBex02acampusfube_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Brett, would you be willing to perform this extension yourself? You could send a p= atch or a Github pull request with the results. Cheers, Manuel ________________________________ From: Brett Bowman [bnbowman@gmail.com] Sent: Sunday, January 11, 2015 6:47 PM To: SeqAn Development Subject: Re: [Seqan-dev] Two Alignment Questions Manuel, I saw the AlignmentStats class when I was digging around in the API for wha= t I need, but I'm afraid it doesn't quite fit: -It doesn't differentiate between Insertions and Deletions (the ratio of wh= ich is important for diagnosing some sequencing problems and bad alignments= ) -It doesn't appear to provide access to the alignment string, meaning I sti= ll need to traverse the whole alignment to generate alternate representatio= ns. -B On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manuel > wrote: Does this help? http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStatshttp://docs.se= qan.de/seqan/develop/?p=3DcomputeAlignmentStats *m ________________________________ From: Brett Bowman [bnbowman@gmail.com] Sent: Saturday, January 10, 2015 3:16 AM To: SeqAn Development Subject: Re: [Seqan-dev] Two Alignment Questions Thanks Rene, >What do you mean by accuracy? What do you need exactly? What I am trying to do is write a tool to align single-molecule sequencing = data (PacBio, Oxford Nanopore) to reference genomes. For which the alignme= nt accuracy and the break-down of the types of errors is very useful, as th= e per-read quality on both platforms varies substantially. What I'd like are member methods or functions-on-alignment-objects to give = the following: -The number of base-pair matches in the alignment -The number of mismatches in the alignment -The number of insertions in the alignment -The number of deletions in the alignment -The alignment string as represented by the Align object's toString() metho= d The first four I need to summarize the similarity of an alignment (i.e. ind= els are likely sequencing error, where as mismatches are likely not), while= the latter is helpful in creating alternate representations for alignments Does that help? -B On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=E9 > wrote: Hey Brett, On 30 Dec 2014, at 21:29, Brett Bowman > wrote: 1) Is there an easy way to get the accuracy of an Alignment object, or is = that something I need to calculate myself? What do you mean by accuracy? What do you need exactly? The Align data structure simply represents the computed alignment. The scor= e is returned by the global align interface. There are several ways to manipulate the alignment of gaps and to compute a= ll best traceback paths. However, those options are not supported on the hi= gh level interfaces but only in the core of the alignment engine. If you tell me what you need exactly we can think of a way to make those in= terfaces public which is planned for the future anyway. But there is no method telling you the accuracy of the =93computed" alignme= nt compared to another =93real=94 alignment. Please, give me some specifics= and we see if we can incorporate this. ... Well, there is a method in the tool seqan-tcoffee, which checks if the comp= uted alignment is correct given the score model and the alignment, but I be= lieve this is not what you are looking for? 2) bandedChainAlignment fails messily when given a Vector of Seeds instead= of a String, where as other functions work fine (e.g. chainSeedsGlobally).= Why does it work for the one and not the other? Excerpt from error messa= ge below. """ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: call= to 'end' is ambiguous SEQAN_ASSERT(itEnd !=3D static_cast(end(seedSet))); ^~~ /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded from m= acro 'SEQAN_ASSERT' (_arg1), # _arg1)) { \ ^ /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: in = instantiation of function template specialization ... /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in instanti= ation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSee= dConfig>, std::allocator, seqan::Def= aultSeedConfig> > >, long, seqan::Tag, seqan::Tag, false, false,= false, false, seqan::Tag >' requested here return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, a= lignConfig, bandExtension); ^ /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in instan= tiation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSee= dConfig>, std::allocator, seqan::Def= aultSeedConfig> > >, long, seqan::Tag, false, false, false, false, seqan::Tag >' requested here long alnScore =3D bandedChainAlignment(alignment, *seedChain, scori= ng, globalConfig); ^ /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation of f= unction template specialization 'RefChainsToAlignments > ()>' requested here auto alignments =3D RefChainsToAlignments(record->Seq, ^ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: candida= te template ignored: substitution failure [with TSeedSet =3D std::vector, seqan::DefaultSeedConfig>, std::allocator, seqan::DefaultSeedConfig> > >] _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) "=94" Ok, this seems to be a bug to me. I=92ll have a look into it. Sincerely, -Brett _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev Bests, Ren=E9 --- Ren=E9 Rahn Ph.D. Student -------------------------------- Tel: (+49) 30 838 75277 Mail: rene.rahn@fu-berlin.de -------------------------------- Institute of Computer Science Algorithmic Bioinformatics (ABI) -------------------------------- Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin -------------------------------- _______________________________________________ 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 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B962867DBex02acampusfube_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Hi Brett,

would you be willing to perform this extension yourself? You could sen= d a patch or a Github pull request with the results.

Cheers,
Manuel

From: Brett Bowman [bnbowman@gmail.com] Sent: Sunday, January 11, 2015 6:47 PM
To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Manuel,

I saw the AlignmentStats class when I was digging around in the API fo= r what I need, but I'm afraid it doesn't quite fit:
-It doesn't differentiate between Insertions and Deletions (the ratio = of which is important for diagnosing some sequencing problems and bad align= ments)
-It doesn't appear to provide access to the alignment string, meaning = I still need to traverse the whole alignment to generate alternate represen= tations.

-B

On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manu= el <manu= el.holtgrewe@fu-berlin.de> wrote:
Does this help?


*m

Fro= m: Brett Bowman [bnbowman@gmail.com]
Sent: Saturday, January 10, 2015 3:16 AM
To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Thanks Rene,

>What do you mean by accuracy? What do you= need exactly? 

What I am trying to do is write a tool to ali= gn single-molecule sequencing data (PacBio, Oxford Nanopore) to reference g= enomes.  For which the alignment accuracy and the break-down of the ty= pes of errors is very useful, as the per-read quality on both platforms varies substantially.

What I'd like are member methods or functions= -on-alignment-objects to give the following:
-The number of base-pair matches in the align= ment
-The number of mismatches in the alignment
-The number of insertions in the alignment
-The number of deletions in the alignment
-The alignment string as represented by the A= lign object's toString() method

The first four I need to summarize the simila= rity of an alignment (i.e. indels are likely sequencing error, where as mis= matches are likely not), while the latter is helpful in creating alternate = representations for alignments

Does that help?

-B

On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=E9 <rene.mae= rker@fu-berlin.de> wrote:
Hey Brett, 


On 30 Dec 2014, at 21:29, Brett Bowman <bnbowman@gmail.com> wrote:

1)  Is there an easy way to get the accuracy of an Alignment obje= ct, or is that something I need to calculate myself?
What do you mean by accuracy? What do you need exactly? 
The Align data structure simply represents the computed alignment. The= score is returned by the global align interface. 
There are several ways to manipulate the alignment of gaps and to comp= ute all best traceback paths. However, those options are not supported on t= he high level interfaces but only in the core of the alignment engine. = ;
If you tell me what you need exactly we can think of a way to make tho= se interfaces public which is planned for the future anyway.
But there is no method telling you the accuracy of the =93computed&quo= t; alignment compared to another =93real=94 alignment. Please, give me some= specifics and we see if we can incorporate this.
...
Well, there is a method in the tool seqan-tcoffee, which checks if the= computed alignment is correct given the score model and the alignment, but= I believe this is not what you are looking for?


2)  bandedChainAlignment fails messily when given a Vector of See= ds instead of a String, where as other functions work fine (e.g. chainSeeds= Globally).  Why does it work for the one and not the other?  Exce= rpt from error message below.

"""
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error:= call to 'end' is ambiguous
    SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator&= gt;(end(seedSet)));
                    =                      = ;               ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded f= rom macro 'SEQAN_ASSERT'
                    =                      = ; (_arg1), # _arg1)) {           \
                    =                      = ;  ^
/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note= : in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in ins= tantiation of function template specialization
      'seqan::bandedChainAlignment<seqan::String<= seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void&= gt; >, seqan::Tag<seqan::ArrayGaps_>,
      std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
      seqan::Tag<seqan::Simple_>, seqan::Tag<s= eqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default= _> >' requested here
    return bandedChainAlignment(align, seedSet, scoreScheme,= scoreScheme, alignConfig, bandExtension);
           ^
/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: no= te: in instantiation of function template specialization
      'seqan::bandedChainAlignment<seqan::String<= seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void&= gt; >, seqan::Tag<seqan::ArrayGaps_>,
      std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
      seqan::Tag<seqan::Simple_>, false, false, f= alse, false, seqan::Tag<seqan::Default_> >' requested here
        long alnScore =3D bandedChainAlignment(ali= gnment, *seedChain, scoring, globalConfig);
                    =     ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in insta= ntiation of function template specialization 'RefChainsToAlignments<seqa= n::AlignConfig<false, true, true, false,
      seqan::Tag<seqan::Default_> > ()>' re= quested here
        auto alignments =3D RefChainsToAlignments(= record->Seq,
                    =       ^
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: ca= ndidate template ignored: substitution failure [with TSeedSet =3D std::vect= or<seqan::Seed<seqan::Tag<seqan::Simple_>,
      seqan::DefaultSeedConfig>, std::allocator<s= eqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>= ; > >]
_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
"=94" 

Ok, this seems to be a bug to me.
I=92ll have a look into it.


Sincerely,
-Brett
_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

Bests, 

Ren=E9 

---

Ren=E9 Rahn
Ph.D. Student
--------------------------------
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=E4t Berlin
Takustra=DFe 9
14195 Berlin
--------------------------------


_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev



_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev


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[137.131.231.56]) by mx.google.com with ESMTPSA id wm1sm275834pac.11.2015.01.14.20.09.38 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Wed, 14 Jan 2015 20:09:39 -0800 (PST) From: Jordan Willis Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Message-Id: <78FDEA2C-1A45-4E14-886D-155F219FF2E2@gmail.com> Date: Wed, 14 Jan 2015 20:18:24 -0800 To: seqan-dev@lists.fu-berlin.de Mime-Version: 1.0 (Mac OS X Mail 7.3 \(1878.6\)) X-Mailer: Apple Mail (2.1878.6) X-Originating-IP: 209.85.192.172 X-ZEDAT-Hint: T X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1421294983-000E8592-8B666371/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.530195, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.8 required=5.0 tests=FREEMAIL_FROM, FU_BOGO_UNSURE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Translate 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, 15 Jan 2015 04:09:45 -0000 Hi Everyone, I was looking through the documentation and couldn=92t find a built-in = translate DNA to amino acid sequence function. Have I not looked hard = enough? J From hannes.hauswedell@fu-berlin.de Thu Jan 15 12:22:37 2015 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YBiVX-003Cio-H3>; Thu, 15 Jan 2015 12:22:35 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.82) with esmtp (envelope-from ) id <1YBiVX-000Ns2-Fs>; Thu, 15 Jan 2015 12:22:35 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.82) with esmtpsa (envelope-from ) id <1YBiVX-001XCy-Er>; Thu, 15 Jan 2015 12:22:35 +0100 From: Hannes Hauswedell To: Jordan Willis Date: Thu, 15 Jan 2015 12:23:16 +0100 Message-ID: <1588924.uOM97ti4K4@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <78FDEA2C-1A45-4E14-886D-155F219FF2E2@gmail.com> References: <78FDEA2C-1A45-4E14-886D-155F219FF2E2@gmail.com> 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::1421320955-000E8592-BA660693/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000031, 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 3.4.0 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: SeqAn Development Subject: Re: [Seqan-dev] Translate 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, 15 Jan 2015 11:22:37 -0000 Am Mittwoch, 14. Januar 2015, 20:18:24 schrieb Jordan Willis: > Hi Everyone, >=20 > I was looking through the documentation and couldn=E2=80=99t find a b= uilt-in > translate DNA to amino acid sequence function. Have I not looked hard= > enough? Dear Jordan, it was not in the last release, but has been in the master and developm= ent=20 branches for quite some time: http://docs.seqan.de/seqan/develop/ -> translate function We will release a new version of SeqAn very soon which will also includ= e the=20 translation module among many other new features. If you need it now, y= ou can=20 checkout either master or develop from github and use that (the version= on=20 develop has a few more features as well as parallelization). Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From bnbowman@gmail.com Thu Jan 22 08:47:30 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1YECUB-000bv9-T1>; Thu, 22 Jan 2015 08:47:28 +0100 Received: from mail-ie0-f172.google.com ([209.85.223.172]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1YECUB-003fkE-HX>; Thu, 22 Jan 2015 08:47:27 +0100 Received: by mail-ie0-f172.google.com with SMTP id rd18so106941iec.3 for ; Wed, 21 Jan 2015 23:47:25 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=P7qHIXwDRZDQ//3P3m+rfoVYtFa5kqHIPi4n86rVkOY=; b=ru+DeI5vdI22betp/BgQThse697k5X3fQtb4/MF2dK/9d1Apjc1RqkcKg3BuZdnJNv QAl8OFYti735XZSQZTEiKZEpcYYsOmH0YianPBHvVArZBQHkweKmJ9juTqqMwX1erRfL NqDucvUBhrAjQ5azNEz5A1Xr0jGuCnaiOb4z8AJWJtBlE7sgoEQRqEJuv99RgUjP2Dd1 aqvVcjNmRFqqMzpQ/Ic2WsCmXP8CTQbADU+tZFkvHtlPGl6NcAJpYGovESWza/9dZ1ma gvJ2ERV0pUsxBNCqRssAfyeBtLVZh6QSuM7pNKB8YEUwrxvMrUg9ixv/gKzmbTKFpDKy lPLA== MIME-Version: 1.0 X-Received: by 10.42.213.7 with SMTP id gu7mr1237047icb.47.1421912844622; Wed, 21 Jan 2015 23:47:24 -0800 (PST) Received: by 10.36.87.85 with HTTP; Wed, 21 Jan 2015 23:47:24 -0800 (PST) In-Reply-To: References: Date: Wed, 21 Jan 2015 23:47:24 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a11c3ab64016351050d38e265 X-Originating-IP: 209.85.223.172 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1421912847-00000D35-F305E914/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.266682, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Two Alignment Questions 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 Jan 2015 07:47:30 -0000 --001a11c3ab64016351050d38e265 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Given an Alignment, how do I get the "TGapSpec" of the underlying rows? I've submitted a pull request with the first half of the features I'd like, now I'm trying to get match strings to work in a generalized way. I'm trying to implement a functions called "alignmentIdentityString", which takes either an Align object, or just two Gaps objects representing rows, and generations a match string with specified characters for matches / mismatches / gaps. It works just fine when I work directly from a supplied Alignment or pair of Rows, but I can't translate an Alignment object down into its component Rows so I can avoid duplicating code. Source gets me the alphabet, and I assume there is a Metafunction to get the Spec of a Gaps/Row object, but the documentation isn't clear and neither Value<> nor GetValue<> appear to give me what I need. """ template String alignmentIdentityString(Align const & align, char const matchChar, char const mismatchChar, char const gapChar) { // Check that the supplied alignment is pairwise SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments."); typedef Align const TAlign; typedef typename Row::Type TGaps; typedef typename Value::Type TGapSpec; // Try #1 //TGaps queryRow =3D row(align, 0); //TGaps referenceRow =3D row(align, 1); // Try #2 Gaps queryRow =3D row(align, 0); Gaps referenceRow =3D row(align, 1); return alignmentSimilarityString(queryRow, referenceRow, scoringScheme, matchChar, mismatchChar, gapChar); } """ What am I missing? -Brett On Mon, Jan 12, 2015 at 1:11 AM, Holtgrewe, Manuel < manuel.holtgrewe@fu-berlin.de> wrote: > Hi Brett, > > would you be willing to perform this extension yourself? You could send > a patch or a Github pull request with the results. > > Cheers, > Manuel > > ------------------------------ > *From:* Brett Bowman [bnbowman@gmail.com] > *Sent:* Sunday, January 11, 2015 6:47 PM > > *To:* SeqAn Development > *Subject:* Re: [Seqan-dev] Two Alignment Questions > > Manuel, > > I saw the AlignmentStats class when I was digging around in the API for > what I need, but I'm afraid it doesn't quite fit: > -It doesn't differentiate between Insertions and Deletions (the ratio of > which is important for diagnosing some sequencing problems and bad > alignments) > -It doesn't appear to provide access to the alignment string, meaning I > still need to traverse the whole alignment to generate alternate > representations. > > -B > > On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manuel < > manuel.holtgrewe@fu-berlin.de> wrote: > >> Does this help? >> >> http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStats >> http://docs.seqan.de/seqan/develop/?p=3DcomputeAlignmentStats >> >> *m >> >> ------------------------------ >> *From:* Brett Bowman [bnbowman@gmail.com] >> *Sent:* Saturday, January 10, 2015 3:16 AM >> *To:* SeqAn Development >> *Subject:* Re: [Seqan-dev] Two Alignment Questions >> >> Thanks Rene, >> >> >What do you mean by accuracy? What do you need exactly? >> >> What I am trying to do is write a tool to align single-molecule >> sequencing data (PacBio, Oxford Nanopore) to reference genomes. For whi= ch >> the alignment accuracy and the break-down of the types of errors is very >> useful, as the per-read quality on both platforms varies substantially. >> >> What I'd like are member methods or functions-on-alignment-objects to >> give the following: >> -The number of base-pair matches in the alignment >> -The number of mismatches in the alignment >> -The number of insertions in the alignment >> -The number of deletions in the alignment >> -The alignment string as represented by the Align object's toString() >> method >> >> The first four I need to summarize the similarity of an alignment (i.e. >> indels are likely sequencing error, where as mismatches are likely not), >> while the latter is helpful in creating alternate representations for >> alignments >> >> Does that help? >> >> -B >> >> On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9 >> wrote: >> >>> Hey Brett, >>> >>> >>> On 30 Dec 2014, at 21:29, Brett Bowman wrote: >>> >>> 1) Is there an easy way to get the accuracy of an Alignment object, >>> or is that something I need to calculate myself? >>> >>> >>> What do you mean by accuracy? What do you need exactly? >>> The Align data structure simply represents the computed alignment. The >>> score is returned by the global align interface. >>> There are several ways to manipulate the alignment of gaps and to >>> compute all best traceback paths. However, those options are not suppor= ted >>> on the high level interfaces but only in the core of the alignment engi= ne. >>> If you tell me what you need exactly we can think of a way to make thos= e >>> interfaces public which is planned for the future anyway. >>> But there is no method telling you the accuracy of the =E2=80=9Ccompute= d" >>> alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Please,= give me some >>> specifics and we see if we can incorporate this. >>> ... >>> Well, there is a method in the tool seqan-tcoffee, which checks if the >>> computed alignment is correct given the score model and the alignment, = but >>> I believe this is not what you are looking for? >>> >>> >>> 2) bandedChainAlignment fails messily when given a Vector of Seeds >>> instead of a String, where as other functions work fine (e.g. >>> chainSeedsGlobally). Why does it work for the one and not the other? >>> Excerpt from error message below. >>> >>> """ >>> /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: >>> call to 'end' is ambiguous >>> SEQAN_ASSERT(itEnd !=3D static_cast(end(seedSet))= ); >>> ^~~ >>> /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded >>> from macro 'SEQAN_ASSERT' >>> (_arg1), # _arg1)) { >>> \ >>> ^ >>> /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: >>> in instantiation of function template specialization >>> >>> ... >>> >>> /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in >>> instantiation of function template specialization >>> >>> 'seqan::bandedChainAlignment>> seqan::Dna5_>, seqan::Alloc >, seqan::Tag, >>> std::vector, >>> seqan::DefaultSeedConfig>, >>> std::allocator, >>> seqan::DefaultSeedConfig> > >, long, >>> seqan::Tag, seqan::Tag, false, >>> false, false, false, seqan::Tag >' requested here >>> return bandedChainAlignment(align, seedSet, scoreScheme, >>> scoreScheme, alignConfig, bandExtension); >>> ^ >>> /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in >>> instantiation of function template specialization >>> >>> 'seqan::bandedChainAlignment>> seqan::Dna5_>, seqan::Alloc >, seqan::Tag, >>> std::vector, >>> seqan::DefaultSeedConfig>, >>> std::allocator, >>> seqan::DefaultSeedConfig> > >, long, >>> seqan::Tag, false, false, false, false, >>> seqan::Tag >' requested here >>> long alnScore =3D bandedChainAlignment(alignment, *seedChain, >>> scoring, globalConfig); >>> ^ >>> /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation >>> of function template specialization >>> 'RefChainsToAlignments>> seqan::Tag > ()>' requested here >>> auto alignments =3D RefChainsToAlignments(record->Seq, >>> ^ >>> /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: >>> candidate template ignored: substitution failure [with TSeedSet =3D >>> std::vector, >>> seqan::DefaultSeedConfig>, >>> std::allocator, >>> seqan::DefaultSeedConfig> > >] >>> _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) >>> "=E2=80=9D" >>> >>> >>> Ok, this seems to be a bug to me. >>> I=E2=80=99ll have a look into it. >>> >>> >>> Sincerely, >>> -Brett >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> >>> >>> Bests, >>> >>> Ren=C3=A9 >>> >>> --- >>> >>> Ren=C3=A9 Rahn >>> Ph.D. Student >>> -------------------------------- >>> Tel: (+49) 30 838 75277 >>> 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 >>> >>> >> >> _______________________________________________ >> 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 > > --001a11c3ab64016351050d38e265 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Given an Alignment, how do I get the "TGapSpec&q= uot; of the underlying rows?

I've submitted a pull = request with the first half of the features I'd like, now I'm tryin= g to get match strings to work in a generalized way.

I&#= 39;m trying to implement a functions called "alignmentIdentityString&q= uot;, which takes either an Align object, or just two Gaps objects represen= ting rows, and generations a match string with specified characters for mat= ches / mismatches / gaps.=C2=A0 It works just fine when I work directly fro= m a supplied Alignment or pair of Rows, but I can't translate an Alignm= ent object down into its component Rows so I can avoid duplicating code.

Source<TGaps> gets me the alphabet, and I assu= me there is a Metafunction to get the Spec of a Gaps/Row object, but the do= cumentation isn't clear and neither Value<> nor GetValue<> = appear to give me what I need.=C2=A0

"&quo= t;"
template <typename TAlphabet, typename TAlignSpe= c>
String<char> alignmentIdentityString(Align<TAlphab= et, TAlignSpec> const & align,
=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0char const matchChar,
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0char cons= t mismatchChar,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0char const gapChar)
{
=C2=A0 =C2=A0= // Check that the supplied alignment is pairwise
=C2=A0 =C2=A0 S= EQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise = alignments.");

=C2=A0 =C2=A0 typedef Align<= ;TAlphabet, TAlignSpec> const TAlign;
=C2=A0 =C2=A0 typedef ty= pename Row<TAlign>::Type TGaps;
=C2=A0 =C2=A0 typedef typen= ame Value<TGaps>::Type TGapSpec;

=C2=A0 =C2= =A0 // Try #1
=C2=A0 =C2=A0 //TGaps queryRow =3D row(al= ign, 0);
=C2=A0 =C2=A0 //TGaps referenceRow =3D row(align, 1);

=C2=A0 =C2=A0 // Try #2
= =C2=A0 =C2=A0 Gaps<TAlphabet, TGapSpec> queryRow =3D row(align, 0);
=C2=A0 =C2=A0 Gaps<TAlphabet, TGapSpec> referenceRow =3D row= (align, 1);

=C2=A0 =C2=A0 return alignmentSi= milarityString(queryRow, referenceRow, scoringScheme,
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0matchChar, mismatchChar, ga= pChar);
}
"""

What am I missing?

-Brett

On Mon, Jan 12, 2015 at 1:11 AM, Holtgrewe, Manuel <man= uel.holtgrewe@fu-berlin.de> wrote:
Hi Brett,

would you be willing to perform this extension yourself? You could sen= d a patch or a Github pull request with the results.

Cheers,
Manuel

Fro= m: Brett Bowman [bnbowman@gmail.com]
Sent: Sunday, January 11, 2015 6:47 PM

To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Manuel,

I saw the AlignmentStats class when I was digging around in the API fo= r what I need, but I'm afraid it doesn't quite fit:
-It doesn't differentiate between Insertions and Deletions (the ra= tio of which is important for diagnosing some sequencing problems and bad a= lignments)
-It doesn't appear to provide access to the alignment string, mean= ing I still need to traverse the whole alignment to generate alternate repr= esentations.

-B

On Sat, Jan 10, 2015 at 2:21 AM, Holtgrewe, Manu= el <manu= el.holtgrewe@fu-berlin.de> wrote:
Does this help?


*m

Fro= m: Brett Bowman [bnbowman@gmail.com]
Sent: Saturday, January 10, 2015 3:16 AM
To: SeqAn Development
Subject: Re: [Seqan-dev] Two Alignment Questions

Thanks Rene,

>What do you mean by accuracy? What do you= need exactly?=C2=A0

What I am trying to do is write a tool to ali= gn single-molecule sequencing data (PacBio, Oxford Nanopore) to reference g= enomes.=C2=A0 For which the alignment accuracy and the break-down of the ty= pes of errors is very useful, as the per-read quality on both platforms varies substantially.

What I'd like are member methods or funct= ions-on-alignment-objects to give the following:
-The number of base-pair matches in the align= ment
-The number of mismatches in the alignment
-The number of insertions in the alignment
-The number of deletions in the alignment
-The alignment string as represented by the A= lign object's toString() method

The first four I need to summarize the simila= rity of an alignment (i.e. indels are likely sequencing error, where as mis= matches are likely not), while the latter is helpful in creating alternate = representations for alignments

Does that help?

-B

On Fri, Jan 9, 2015 at 12:51 AM, Rahn, Ren=C3=A9= <rene.mae= rker@fu-berlin.de> wrote:
Hey Brett,=C2=A0


On 30 Dec 2014, at 21:29, Brett Bowman <bnbowman@gmail.com> wrote:

1) =C2=A0Is there an easy way to get the accuracy of an Alignment obje= ct, or is that something I need to calculate myself?
What do you mean by accuracy? What do you need exactly?=C2=A0
The Align data structure simply represents the computed alignment. The= score is returned by the global align interface.=C2=A0
There are several ways to manipulate the alignment of gaps and to comp= ute all best traceback paths. However, those options are not supported on t= he high level interfaces but only in the core of the alignment engine.=C2= =A0
If you tell me what you need exactly we can think of a way to make tho= se interfaces public which is planned for the future anyway.
But there is no method telling you the accuracy of the =E2=80=9Ccomput= ed" alignment compared to another =E2=80=9Creal=E2=80=9D alignment. Pl= ease, give me some specifics and we see if we can incorporate this.
...
Well, there is a method in the tool seqan-tcoffee, which checks if the= computed alignment is correct given the score model and the alignment, but= I believe this is not what you are looking for?


2) =C2=A0bandedChainAlignment fails messily when given a Vector of See= ds instead of a String, where as other functions work fine (e.g. chainSeeds= Globally).=C2=A0 Why does it work for the one and not the other?=C2=A0 Exce= rpt from error message below.

"""
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error:= call to 'end' is ambiguous
=C2=A0 =C2=A0 SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator&= gt;(end(seedSet)));
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded f= rom macro 'SEQAN_ASSERT'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 (_arg1), # _arg1)) { =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 \
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0^
/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note= : in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in ins= tantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, seqan::Tag<s= eqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default= _> >' requested here
=C2=A0 =C2=A0 return bandedChainAlignment(align, seedSet, scoreScheme,= scoreScheme, alignConfig, bandExtension);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^
/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in i= nstantiation of function template specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >, seqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<seqan= ::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed&= lt;seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >= , long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>, false, false, f= alse, false, seqan::Tag<seqan::Default_> >' requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 long alnScore =3D bandedChainAlignment(ali= gnment, *seedChain, scoring, globalConfig);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation= of function template specialization 'RefChainsToAlignments<seqan::A= lignConfig<false, true, true, false,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Default_> > ()>'= ; requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 auto alignments =3D RefChainsToAlignments(= record->Seq,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 ^
/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: ca= ndidate template ignored: substitution failure [with TSeedSet =3D std::vect= or<seqan::Seed<seqan::Tag<seqan::Simple_>,
=C2=A0 =C2=A0 =C2=A0 seqan::DefaultSeedConfig>, std::allocator<s= eqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>= ; > >]
_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
"=E2=80=9D"=C2=A0

Ok, this seems to be a bug to me.
I=E2=80=99ll have a look into it.


Sincerely,
-Brett
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Bests,=C2=A0

Ren=C3=A9=C2=A0

---

Ren=C3=A9 Rahn
Ph.D. Student
--------------------------------
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin
Takustra=C3=9Fe 9
14195 Berlin
--------------------------------


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