From bernd.jagla@pasteur.fr Tue Oct 08 09:02:23 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VTRJG-001sL2-0a>; Tue, 08 Oct 2013 09:02:22 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VTRJF-00258V-UF>; Tue, 08 Oct 2013 09:02:21 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 66B59381054 for ; Tue, 8 Oct 2013 09:02:20 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zodiac.pt2.pasteur.fr [157.99.241.45]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 2D36F381051 for ; Tue, 8 Oct 2013 09:02:20 +0200 (CEST) Message-ID: <5253ADF9.6090004@pasteur.fr> Date: Tue, 08 Oct 2013 09:02:17 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20130911 Thunderbird/17.0.9 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1381215742-00000AAA-6AA1F2A5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] cmake - java version ? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 08 Oct 2013 07:02:23 -0000 Hi, when executing "cmake ." I get the following warning: -- Warning, could not run java --version when trying to run java, I see it is installed (not a given... ) but there is no option "--version" just "-version" Here is what is installed: java version "1.7.0_25" OpenJDK Runtime Environment (rhel-2.3.10.4.el6_4-x86_64) OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode) I guess it is not that important... Anyways any idea on how to remove this warning is appreciated... Thanks, Bernd From jakob.schulze@fu-berlin.de Thu Oct 17 20:04:05 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VWrvX-003MIS-VJ>; Thu, 17 Oct 2013 20:04:04 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VWrvX-003zHo-Th>; Thu, 17 Oct 2013 20:04:03 +0200 Received: from dslb-178-005-012-102.pools.arcor-ip.net ([178.5.12.102] helo=[192.168.2.104]) by inpost2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1VWrvX-002a9Y-QR>; Thu, 17 Oct 2013 20:04:03 +0200 Message-ID: <5260268B.70107@fu-berlin.de> Date: Thu, 17 Oct 2013 20:03:55 +0200 From: Jakob Schulze User-Agent: Mozilla/5.0 (X11; Linux i686; rv:24.0) Gecko/20100101 Thunderbird/24.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 178.5.12.102 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1382033043-00000966-6ADFB73E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.283251, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] File into pattern matching X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 17 Oct 2013 18:04:05 -0000 Hey, I am trying to search a bunch of patterns (e.g. 'chr9\t30594839\t') in a 40 GB samtools pileup file. (one record each line, containing position and mapping data) Unfortunately the samtools flag -r for partial pileup seems to be broken, so I am left searching in the huge complete file. Is there a way to directly pass a file stream as a haystack to Finder? Something like this? Finder finder(inStream); Using a recordreader to read file line by line takes forever: std::fstream inStream(argv[1], std::ios::binary | std::ios::in); seqan::RecordReader > reader(inStream); String needles; Pattern, MultiBfam> pattern(needles); while (!atEnd(reader)) { int res = readLine(line, reader); Finder finder(line); } Best Regards, Jakob Btw: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSystem is totally awesome, it took me a flash to get it running with Makefiles. However, I just noticed that the link to "Use your own build system" under http://trac.seqan.de/ --> Howtos seems to be broken. From manuel.holtgrewe@fu-berlin.de Fri Oct 18 09:13:30 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VX4FV-000JwQ-0G>; Fri, 18 Oct 2013 09:13:29 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VX4FU-002Ep0-UZ>; Fri, 18 Oct 2013 09:13:28 +0200 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VX4FU-001hTn-Ip>; Fri, 18 Oct 2013 09:13:28 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0158.001; Fri, 18 Oct 2013 09:13:27 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] File into pattern matching Thread-Index: AQHOy2NJg4rxajLy3kekG2liP/9OgZn6DC3W Message-ID: References: <5260268B.70107@fu-berlin.de> In-Reply-To: <5260268B.70107@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Fri, 18 Oct 2013 09:13:26 +0200 X-Original-Date: Fri, 18 Oct 2013 07:13:26 +0000 X-Originating-IP: 130.133.170.201 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1382080409-00000966-49328B93/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.335045, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] File into pattern matching X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 18 Oct 2013 07:13:30 -0000 Consider using awk or grep for such tasks since they are specialized for su= ch cases.=0A= =0A= I fixed/removed the link on the Trac start page.=0A= =0A= HTH,=0A= Manuel=0A= ________________________________________=0A= From: Jakob Schulze [jakob.schulze@fu-berlin.de]=0A= Sent: Thursday, October 17, 2013 8:03 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] File into pattern matching=0A= =0A= Hey,=0A= I am trying to search a bunch of patterns (e.g. 'chr9\t30594839\t') in a=0A= 40 GB samtools pileup file.=0A= (one record each line, containing position and mapping data)=0A= =0A= Unfortunately the samtools flag -r for partial pileup seems to be=0A= broken, so I am left searching in the huge complete file.=0A= Is there a way to directly pass a file stream as a haystack to Finder?=0A= =0A= Something like this?=0A= Finder finder(inStream);=0A= =0A= =0A= Using a recordreader to read file line by line takes forever:=0A= =0A= std::fstream inStream(argv[1], std::ios::binary | std::ios::in);=0A= seqan::RecordReader > reader(inStream);= =0A= String needles;=0A= Pattern, MultiBfam> pattern(needles);=0A= while (!atEnd(reader)) {=0A= int res =3D readLine(line, reader);=0A= Finder finder(line);=0A= }=0A= =0A= =0A= Best Regards,=0A= Jakob=0A= =0A= Btw: http://trac.seqan.de/wiki/BuildManual/IntegrationWithYourOwnBuildSyste= m=0A= is totally awesome, it took me a flash to get it running with Makefiles.=0A= However, I just noticed that the link to "Use your own build system"=0A= under http://trac.seqan.de/ --> Howtos seems to be broken.=0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From manuel.holtgrewe@fu-berlin.de Tue Oct 22 09:15:24 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VYWBW-003yMb-Kj>; Tue, 22 Oct 2013 09:15:22 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VYWBW-000jmO-Im>; Tue, 22 Oct 2013 09:15:22 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VYWBW-002yFp-72>; Tue, 22 Oct 2013 09:15:22 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0158.001; Tue, 22 Oct 2013 09:15:21 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] cmake - java version ? Thread-Index: AQHOw/RajrAlLIPd2E6EKr0j0DjG5poAZDCU Message-ID: References: <5253ADF9.6090004@pasteur.fr> In-Reply-To: <5253ADF9.6090004@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Tue, 22 Oct 2013 09:15:19 +0200 X-Original-Date: Tue, 22 Oct 2013 07:15:19 +0000 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1382426122-00000966-381C91DA/0-0/0-0 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 X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] cmake - java version ? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 Oct 2013 07:15:24 -0000 Hi Bernd,=0A= =0A= yes, we only need Java for CTD packacking since the jar command included wi= th the JDK distribution allows us to create ZIP files (jar files are just z= ip files).=0A= =0A= We use CMake's standard find_package script that gets installed when you in= stall CMake on your Linux. This in turn means that the problem is 99.99% on= the side of your CMake version or the software installation on your Linux = boxen....=0A= =0A= Looking into the FindJava.cmake file it looks like it's only a problem in C= Make's error message (see bottom).=0A= =0A= To fix this, you would have to install the JDK.=0A= =0A= HTH,=0A= Manuel=0A= =0A= IF(Java_JAVA_EXECUTABLE)=0A= EXECUTE_PROCESS(COMMAND ${Java_JAVA_EXECUTABLE} -version=0A= RESULT_VARIABLE res=0A= OUTPUT_VARIABLE var=0A= ERROR_VARIABLE var # sun-java output to stderr=0A= OUTPUT_STRIP_TRAILING_WHITESPACE=0A= ERROR_STRIP_TRAILING_WHITESPACE)=0A= IF( res )=0A= IF(${Java_FIND_REQUIRED})=0A= MESSAGE( FATAL_ERROR "Error executing java -version" )=0A= ELSE()=0A= MESSAGE( STATUS "Warning, could not run java --version")=0A= ENDIF()=0A= ELSE()=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Tuesday, October 08, 2013 9:02 AM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] cmake - java version ?=0A= =0A= Hi,=0A= =0A= when executing "cmake ." I get the following warning:=0A= =0A= -- Warning, could not run java --version=0A= =0A= when trying to run java, I see it is installed (not a given... ) but=0A= there is no option "--version" just "-version"=0A= =0A= Here is what is installed:=0A= =0A= java version "1.7.0_25"=0A= OpenJDK Runtime Environment (rhel-2.3.10.4.el6_4-x86_64)=0A= OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)=0A= =0A= I guess it is not that important...=0A= =0A= Anyways any idea on how to remove this warning is appreciated...=0A= =0A= Thanks,=0A= =0A= Bernd=0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A=