source: trunk/yat/omic

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Diff Rev Age Author Log Message
(edit) @3068   9 years Peter Fixes #766 Replace #defines HAVE_BAM_H (and friends) in …
(edit) @3056   9 years Peter fixes #764: throw if region in BamReadIterator? is invalid
(edit) @3055   9 years Peter closes #746. New function BamRead::name(1)
(edit) @3052   9 years Peter remove empty line
(edit) @3048   9 years Peter avoid cassert in header file
(edit) @3032   9 years Peter refs #746. Simplify cigar function using logic similar to sequence(2). …
(edit) @3031   9 years Peter new function BamRead::sequence(2). refs #746
(edit) @3030   9 years Peter refs #746. avoid false positive throws
(edit) @3029   9 years Peter refs #746. Add docs and throw in aux_del if tag is absent (rather than …
(edit) @3028   9 years Peter functions to access, append, and remove aux field. refs #746
(edit) @3026   9 years Peter add function to modify a base quality (BamRead?). refs #746
(edit) @3018   9 years Peter merge patch release 0.10.2 into trunk
(edit) @2999   9 years Peter closes #739. Two new functions in BamHeader?: tid(string) and parse_region.
(edit) @2994   9 years Peter new class BamReadFilter?. closes #738
(edit) @2993   9 years Peter conform GPL header to same style as in other yat files
(edit) @2990   9 years Peter always install bam headers, but #error out noisily if included when …
(edit) @2989   9 years Peter speedup BamRead::cigar for case when size is not modified.
(edit) @2988   9 years Peter bam1_seq_seti was not defined in samtools 0.1.18. This workarounds …
(edit) @2986   9 years Peter merge 0.10-stable branch into trunk
(edit) @2985   9 years Peter refs #746. added function to modify one element in sequence
(edit) @2983   9 years Peter fixes #751. throw if OutBamFile::write fails
(edit) @2980   9 years Peter add syntax-check rule (included in maintainer-check), add two missing …
(edit) @2978   9 years Peter fix docs typos
(edit) @2960   9 years Peter merge patch release 0.10.1 into trunk
(edit) @2949   9 years Peter comments describing defines from bam.h
(edit) @2943   9 years Peter merge release 0.10 into trunk
(edit) @2932   9 years Peter remove misleading comment as these files are no longer direct input to …
(edit) @2919   9 years Peter update copyright years
(edit) @2911   9 years Peter accidently included in r2910
(edit) @2910   9 years Peter improve docs. closes #729
(edit) @2905   9 years Peter remove superfluous 'using'
(edit) @2904   9 years Peter boost concept check. refs #729
(edit) @2903   9 years Peter refs #729. document bam_pair_analyse
(edit) @2902   9 years Peter test for bam_pair_analyse. refs #729
(edit) @2900   9 years Peter remove trailing WS
(edit) @2899   9 years Peter function bam_pair_analyse
(edit) @2897   9 years Peter prefer throwing yat::utility::runtime_error. refs #729
(edit) @2896   9 years Peter improve doc and remove private classes from docs
(edit) @2895   9 years Peter add two tests for bam functionality
(edit) @2891   9 years Peter check for samtools in configure; create bam file in 'make check' if we …
(edit) @2887   9 years Peter docs typo
(edit) @2886   9 years Peter fast swap for BamRead?
(edit) @2884   9 years Peter add missing since tags. refs #729
(edit) @2883   9 years Peter New classes to wrap around functionality provided by samtools. refs #729
(edit) @2881   10 years Peter Define PP variables in config.h rather than in CPPFLAGS. Include …
(edit) @2824   10 years Peter remove intermediate libraries. Makefiles in corresponding …
(edit) @2787   10 years Peter update coyright years
(edit) @2773   10 years Peter declare HEADERs with srcdir so doxygen understands where to find them …
(edit) @2763   10 years Peter avoid race with static variable
(edit) @2749   10 years Peter add small convenience Makefiles in subdirs. closes #703
(edit) @2743   10 years Peter correct doc typo
(edit) @2742   10 years Peter minor speedup in DNA::complement
(edit) @2741   10 years Peter prefer vector and string as internals in omic::DNA
(edit) @2739   10 years Peter refs #703 using a non-recursive Makefile. Old Makefile.am are kept but …
(edit) @2723   10 years Peter avoid < with string::npos
(edit) @2703   10 years Peter merge release 0.8.1 into trunk
(edit) @2677   10 years Peter remove trailing WS
(edit) @2608   11 years Peter delete trailing newlines
(edit) @2596   11 years Peter comment language
(edit) @2591   11 years Peter updating copyright years
(edit) @2577   11 years Peter closes #672
(edit) @2576   11 years Peter avoid warning with doxygen 1.7.5.1
(edit) @2573   11 years Peter avoid long line
(edit) @2482   11 years Peter new class GFF. closes #647
(edit) @2470   11 years Peter merge patch release 0.7.2 into trunk
(edit) @2441   11 years Peter docs typo
(edit) @2389   11 years Peter adding some missing since tags
(edit) @2388   11 years Peter add doxygen tag relates
(edit) @2387   11 years Peter avoid long lines
(edit) @2385   11 years Peter doc typo
(edit) @2377   11 years Peter docs typo
(edit) @2369   11 years Peter fixes some issues in class Codon and extending tests
(edit) @2368   11 years Peter new class omic::Codon
(edit) @2366   11 years Peter New class GenomicPosition?
(edit) @2342   12 years Peter adding missing files. refs #377
(add) @2341   12 years Peter New namespace omic and new class omic::DNA. closes #377
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