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Creating a custom GATK Walker (GATK 3.6) : my notebook. This is my notebook for creating a custom engine in GATK. I want to read a VCF file and to get a table of category/count. Something like this:. I create a class Category. Describing each row in the table. It's just a List of Strings. Labels ; Category. As were going to use Category. In an associative array / Map we need to implement. Implementing hashCode and equals. Labels ; Category. Labels); } @Override. HashCode(); } @Override. Get(i) ; if.

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YOKOFAKUN | plindenbaum.blogspot.com Reviews

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Creating a custom GATK Walker (GATK 3.6) : my notebook. This is my notebook for creating a custom engine in GATK. I want to read a VCF file and to get a table of category/count. Something like this:. I create a class Category. Describing each row in the table. It's just a List of Strings. Labels ; Category. As were going to use Category. In an associative array / Map we need to implement. Implementing hashCode and equals. Labels ; Category. Labels); } @Override. HashCode(); } @Override. Get(i) ; if.

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YOKOFAKUN | plindenbaum.blogspot.com Reviews

https://plindenbaum.blogspot.com

Creating a custom GATK Walker (GATK 3.6) : my notebook. This is my notebook for creating a custom engine in GATK. I want to read a VCF file and to get a table of category/count. Something like this:. I create a class Category. Describing each row in the table. It's just a List of Strings. Labels ; Category. As were going to use Category. In an associative array / Map we need to implement. Implementing hashCode and equals. Labels ; Category. Labels); } @Override. HashCode(); } @Override. Get(i) ; if.

INTERNAL PAGES

plindenbaum.blogspot.com

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YOKOFAKUN: Playing with the #GA4GH schemas and #Avro : my notebook

http://plindenbaum.blogspot.com/2015/06/playing-with-ga4gh-schemas-and-avro-my.html

Playing with the #GA4GH schemas and #Avro : my notebook. After watching David Haussler's talk "Beacon Project and Data Sharing ApIs". I wanted to play with Avro. And the models and APIs defined by the Global Alliance for Genomics and Health (ga4gh). Coalition Here is my notebook. Avro is a remote procedure call and data serialization framework developed within Apache's Hadoop. Project. It uses JSON. First, we download the java tools. And libraries for apache Avro. Next, we download the schemas. Curl -L -...

2

YOKOFAKUN: December 2014

http://plindenbaum.blogspot.com/2014_12_01_archive.html

Divide-and-conquer in a #Makefile : recursivity and #parallelism. This post is my notebook about implementing a divide-and-conquer strategy. Say you have a list of 'N' VCFs. Files You want to create a list of:. Common SNPs in vcf1 and vcf2. Common SNPs in vcf3 and the previous list. Common SNPs in vcf4 and the previous list. Common SNPs in vcfN and the previous list. Yes, I know I can do this using:. Grep -v ' #' f.vcf cut -f 1,2,4,5 sort uniq. Using a linear Makefile. It could look like:. XML XSLT = #Ma...

3

YOKOFAKUN: January 2015

http://plindenbaum.blogspot.com/2015_01_01_archive.html

Filtering Fasta Sequences using the #NCBI C API. My notebook. In my previous post ( http:/ plindenbaum.blogspot.com/2015/01/compiling-c-hello-world-program-using.html. I've built a simple Hello World application using the. Http:/ www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP DOC/. Here, I'm gonna to extend the code in order to create a program filtering FASTA sequences on their sizes. Needs three new arguments:. Min size of the fasta sequence. Max size of the fasta sequence. The method FastaFilterSize: Init().

4

YOKOFAKUN: February 2015

http://plindenbaum.blogspot.com/2015_02_01_archive.html

Integrating a java program in #usegalaxy. This is my notebook for the integration of java. Programs in https:/ usegalaxy.org/. Create a directory for your tools under. Put all the required jar. Files and the XML. Files describing your tools (see below) in this new directory:. Each tool is described with a XML. File whose schema is available at: https:/ wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax. For example here is a simple file describing the tool VcfHead. Number of variants ". Gunzip -c ${inpu...

5

YOKOFAKUN: Inside the Variation Toolkit: Tools for Gene Ontology

http://plindenbaum.blogspot.com/2012/01/inside-variation-toolkit-tools-for-gene.html

Inside the Variation Toolkit: Tools for Gene Ontology. Is a C tool that is part of my experimental Variation Toolkit. This program is a set of tools for GeneOntology. It is based on the sqlite3. Download the sources from Google-Code using subversion:. Svn checkout http:/ variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only. Or update the sources of an existing installation. Cd variationtoolkit svn update. Http:/ www.sqlite.org/. Libraries and headers for sqlite3. Curl -s "ftp:/ ftp.e...

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triggXR: Cabin Fever

http://www.triggxr.com/2008/12/cabin-fever.html

Less mystery, more me. Sunday, December 21, 2008. I thought he was going to cry when I gave him the 100 bucks. It's not often you get to see money solve a problem in person. He showed me his lower lip which had two large cuts and was very swollen. I told him I was putting a blessing on him for being such a good Samaritan. Fortunately the cat turned around and came back in the house. I guess the litter box doesn't seem so bad under the circumstances. Posted by XR trigg. Subscribe to: Post Comments (Atom).

kemistry-desktop.blogspot.com

kemistry desktop environment: June 2008

http://kemistry-desktop.blogspot.com/2008_06_01_archive.html

Saturday, June 07, 2008. Fish: my next generation sh? In a nice write up of functionality. Nice tip! I have been using BASH for a long time now, before which I used csh, IIRC. Oi, that was on the old Solaris days. Anyway, default settings are quite nice, but one thing I don't like so much is the abbreviated pwd. In the prompt. At least, not for the full prompt. It would suite me best of the last two or three directories were not abbreviated, but could not find an option for that. Instead of prompt pwd.

igotgenes.blogspot.com

It's Not Easy Being Genes: January 2011

http://igotgenes.blogspot.com/2011_01_01_archive.html

It's Not Easy Being Genes. Friday, January 7, 2011. Common Good: Adding a Creative Commons License button to your Blogspot (Blogger) blog. I have intended to place the contents of this blog under a Creative Commons (CC) license. For a long while, especially given that all the attractive photos I love to use in these blog entries come from Creative Commons-licensed content on Flickr. For those unfamiliar with Creative Commons licenses. They explicitly permit re-use of creative works a priori. Go to your b...

igotgenes.blogspot.com

It's Not Easy Being Genes: July 2009

http://igotgenes.blogspot.com/2009_07_01_archive.html

It's Not Easy Being Genes. Wednesday, July 1, 2009. Getting the hostname back in the Jaunty GDM greeter. Release, 9.04, codename " Jaunty Jackelope. Has turned out to be one of the best, maybe even on par with the "Gutsy Gibbon" release. The aesthetics definitely got some love; for example, if you're not running the "Dust" theme, you're missing out. [Hint: go to Preferences. And select "Dust"] The GDM greeter login screen looks the best of any Ubuntu release. To use this patch, just do. Links to this post.

semantichumanities.wordpress.com

Algorithms for Matching Strings | Semantic Humanities

https://semantichumanities.wordpress.com/2006/08/30/algorithms-for-matching-name-variants

Algorithms for Matching Strings. August 30, 2006 at 2:59 pm · Filed under Scripting. Last year, I had database table full of authors’ names I’d entered in from various sources. Many of these names were simply variants of one another: eg. I had already associated many of these names with biographical information in another table. My problem now was to match up the unidentified name variants with the identified names. Mr John H. Smith. Levenshtein('Smith', 'Smyth'); / returns 1. So I subtract the. Levensht...

lindenb.tumblr.com

tyeul:Source: @WildeThinks by @dvanzuijlekom.... | Yokofakun

http://lindenb.tumblr.com/post/126283754685/tyeul-source-wildethinks-by-dvanzuijlekom

Http:/ plindenbaum.blogspot.com. August 9, 2015. Page 1 of 1.

hackathon2.dbcls.jp

Participants – BioHackathon 2009

http://hackathon2.dbcls.jp/wiki/Participants

Marine Genomics Unit, OIST, Japan). TogoWS, BioRuby, Galaxy i18n,. Kazusa DNA Res, Japan). Keiko Sakuma (DBCLS, Japan). Eiji Ueda (DBCLS, Japan). Director of Marine Genomics Unit, OIST, Japan). Director of DBCLS, Japan). Yoshiki Hotta (Director of ROIS, Japan). Galaxy; Emory Univ, US). Galaxy; Penn State Univ, US). BioMart; OICR, Canada). BioMart/GMOD; EBI, UK). Univ of Granada, Spain). Univ of Granada, Spain). MOWserv, mAPI, jORCA, Magallanes; Universidad de Málaga, Spain). José M. Fernández. Inst Adv&#...

davidrothman.net

PubMed Preview | davidrothman.net

http://davidrothman.net/2009/09/29/pubmed-preview

Skip to primary content. Skip to secondary content. Popular Bits of Geekery. List of Medical Wikis. Consumer Health and Patient Education Information Search Engine. History of Medicine Search Engine. Medical Library Search Engine. September 29, 2009. Http:/ preview.ncbi.nlm.nih.gov/sites/pubmed. First impression: TONS of wasted screen real estate on that front page. What do you think? Thanks to Patricia Anderson for the heads up! Patricia’s take is here. This entry was posted in For Medical Libraryfolk.

researchremix.wordpress.com

Importing PubMed MEDLINE details into mySQL database | Research Remix

https://researchremix.wordpress.com/2008/08/15/importing-pubmed-medline-details-into-mysql-database

August 15, 2008. Importing PubMed MEDLINE details into mySQL database. 8212; Tags: text mining. 8212; Heather Piwowar @ 12:45 pm. One more post in my blogging-spree:. I’m doing some text-mining with PubMed MeSH terms, titles, and abstracts. I’ve written quick-and-dirty scripts to parse and analyze PubMed citations before… but enough already. I need a reusable, stable system. Enter Java, Weka, and mySQL. Tools for loading Medline into a local relational database. Use a database. I originally thought I...

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Marți, 1 august 2017. La rencontre des mondes/ vernisaj/ 1 iulie 2017/ Cherbourg-en-Cotentin/Abbaye du Voeu. Marți, august 01, 2017. Ramona si Mihai Chitu/ Plin de martieni/ 2017/ marker pe hartie. Marți, august 01, 2017. Abonați-vă la: Postări (Atom). Suntem impreuna din 2005 si deabia acum declaram oficial aceasta legatura. Speram sa ne bucuram cat mai mult timp de prezenta lor printre noi si daca vreti sa infiati si voi cate un martian nu ezitati sa ne contactati. La rencontre des mondes.

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YOKOFAKUN

Creating a custom GATK Walker (GATK 3.6) : my notebook. This is my notebook for creating a custom engine in GATK. I want to read a VCF file and to get a table of category/count. Something like this:. I create a class Category. Describing each row in the table. It's just a List of Strings. Labels ; Category. As were going to use Category. In an associative array / Map we need to implement. Implementing hashCode and equals. Labels ; Category. Labels); } @Override. HashCode(); } @Override. Get(i) ; if.

plindepoeme.skyrock.com

Blog de plindepoeme - que des poemes - Skyrock.com

Mot de passe :. J'ai oublié mon mot de passe. Mise à jour :. Abonne-toi à mon blog! Je voudrais lui parler. Mais je ne fais que m'enfarger. M'enfarger dans mes mots. Qui remplissent ce sceau. Pour qu'enfin les mots sortent. Pour l'instant ils ne font que s'empiler. Et l'empêche de déborder. Je rêve tout bas. Que je suis dans ses bras. Mais ce n'est qu'un rêve. Sont comme les cieux. Quand je ferme les yeux. Ou poster avec :. Posté le mardi 20 décembre 2005 12:00. Modifié le lundi 03 juillet 2006 18:13.

plindeptishet.skyrock.com

Blog de plindeptishet - (((°°°~~Blog sur vos shetlands~~°°°))) - Skyrock.com

Mot de passe :. J'ai oublié mon mot de passe. Blog sur vos shetlands ) ). Voila alors j'avait envi de faire un blog sur c piti shetland! Donc comme je n'en ai pas ba vous trouverer dans se blog plin de petits shetland,et si vous vouler que le votre y soi ossi sur se blog laisser un comms en disan que vous vouler mettre votre shet dessu,et votre adress email ou votr blog pour que je puisse repondre! Mise à jour :. Abonne-toi à mon blog! Ou poster avec :. Posté le mardi 24 octobre 2006 15:06. N'oublie pas ...