Opened 9 years ago

Closed 9 years ago

#729 closed request (fixed)

samtools wrapper classes

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.10
Component: omic Version: trunk
Keywords: Cc:

Description

samtools C api is very useful to handle bamfiles but the API requires a lot of manual allocation and deallocation of its structs, which is not very C++ friendly. In order to use this functionality in a C++ context e.g. in std::vector one need to have wrapper classes around these structs in same fashion as Matrix and Vector are wrappers around GSL structs.

Change History (17)

comment:1 Changed 9 years ago by Peter

Component: utilitybam
Owner: changed from Jari Häkkinen to Peter

comment:2 Changed 9 years ago by Peter

(In [2864]) file structure and empty automake file for new bam namespace. refs #729

comment:3 Changed 9 years ago by Peter

(In [2868]) refs #729. Add configure tests for samtools

comment:4 Changed 9 years ago by Peter

(In [2869]) improve error messages. emove debug code. refs #729

comment:5 Changed 9 years ago by Peter

Component: bamomic

comment:6 Changed 9 years ago by Peter

(In [2874]) remove namespace bam. bam stuff will be put in omic namespace instead. refs #729

comment:7 Changed 9 years ago by Peter

(In [2883]) New classes to wrap around functionality provided by samtools. refs #729

comment:8 Changed 9 years ago by Peter

If configured --without-samtools Bam support is not compiled into libyat. For that reason, I chose to exclude Bam* header files from both installation and Doxygen input in that case. Is this desired behaviour? If not, it can easily be changed. (changing only one and not both a bit more tricky but doable.)

comment:9 Changed 9 years ago by Peter

(In [2884]) add missing since tags. refs #729

comment:10 Changed 9 years ago by Peter

(In [2888]) add example SAM file. refs #729

comment:11 Changed 9 years ago by Peter

(In [2891]) check for samtools in configure; create bam file in 'make check' if we have samtools. refs #729

comment:12 Changed 9 years ago by Peter

Status: newassigned

comment:13 Changed 9 years ago by Peter

(In [2897]) prefer throwing yat::utility::runtime_error. refs #729

comment:14 Changed 9 years ago by Peter

(In [2902]) test for bam_pair_analyse. refs #729

comment:15 Changed 9 years ago by Peter

(In [2903]) refs #729. document bam_pair_analyse

comment:16 Changed 9 years ago by Peter

(In [2904]) boost concept check. refs #729

comment:17 Changed 9 years ago by Peter

Resolution: fixed
Status: assignedclosed

(In [2910]) improve docs. closes #729

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