For example, HTSJDK is the Java equivalent and is used extensively in Java applications Sambamba is written in the D language and focuses primarily on efficient multi-threaded work Scramble has BAM and SAM capability and is the primary source for experimental CRAM development and JBrowse implements read-only support for multiple formats in JavaScript. Numerous other tools have been developed since then in a wide variety of programming languages. The SAM/BAM format originally came with a reference implementation, SAMtools, and VCF/BCF with VCFtools and BCFtools (then part of the SAMtools package). Later, in 2011, as the number of sequenced samples increased and the text format proved too slow to parse, a binary version BCF (see Supplementary Fig. In 2010, a Variant Call Format (VCF) was introduced for storing genetic variation. SAM/BAM quickly replaced all the other short-read alignment formats and became the de facto standard in the analysis of high-throughput sequence data. Towards the end of 2008 the subgroup announced the first SAM specification, detailing a text-based SAM format and its binary representation, the BAM format. In a conference call on 21 October 2008, the 1000 Genomes Project analysis subgroup decided to take on the issue by unifying a variety of short-read alignment formats into the Sequence Alignment/Map format (SAM).
This fragmented ecosystem hampered the collaboration between the participants of the project and delayed the development of advanced data analysis algorithms. Users were forced to implement bespoke format converters to bridge tools, and because formats encoded different information, this was time consuming, laborious, and sometimes impossible. Each of them had its own input or output format for limited use cases, and interoperability was a major challenge.
#Klib library python install#
Trying to follow up with sudo pip install pandas -upgrade gives the same results as above.When the 1000 Genomes Project was launched in early 2008, there were many short-read aligners and variant callers. I have tried the alternative route of sudo apt-get install python-pandas which does install pandas but it's only version 0.8 rather than 0.13.
What is going on here and how do I fix it? It never actually fails, but doesn't complete either in over half an hour. Pandas/src/klib/khash_python.h:49:1: warning: statement with no effect Īnd then more errors warnings for a long time. Pandas/src/klib/khash_python.h: In function âkh_del_strboxâ: Pandas/src/klib/khash_python.h:44:1: warning: statement with no effect Pandas/src/klib/khash_python.h: In function âkh_del_pysetâ: Pandas/src/klib/khash_python.h:38:1: warning: statement with no effect Pandas/src/klib/khash_python.h: In function âkh_del_pymapâ: Pandas/src/klib/khash_python.h:13:1: warning: statement with no effect Warning: no previously-included files matching '*.png' found anywhere in distribution
Warning: no previously-included files matching '.DS_Store' found anywhere in distribution Warning: no previously-included files matching '.git*' found anywhere in distribution Warning: no previously-included files matching '*.pyc' found anywhere in distribution Warning: no previously-included files matching '*.pyd' found anywhere in distribution Warning: no previously-included files matching '*.so' found anywhere in distribution No previously-included directories found matching 'doc/build' Warning: no files found matching 'README.rst' Running setup.py egg_info for package pandas
~ $ pip install pandasĭownloading pandas-0.13.1.tar.gz (6.1Mb): 6.1Mb downloaded I'm trying to install Python Pandas on my Raspi and I'm finding strange errors.
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