Changeset 3364


Ignore:
Timestamp:
Nov 25, 2014, 2:17:50 PM (8 years ago)
Author:
Peter
Message:

describe htslib support in NEWS and README. refs #794

Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/NEWS

    r3342 r3364  
    77  - utility::Range is deprecated (ticket #786)
    88  - AveragerWeighted::n(void) now return 0, when object is empty (ticket #802)
     9  - added support for htslib (see ticket #794)
    910
    1011  A complete list of closed tickets can be found here [[br]]
  • trunk/README

    r3114 r3364  
    102102== Optional packages ==
    103103
    104 === Samtools ===
    105 
    106 Samtools available from http://samtools.sourceforge.net/ is required
    107 to enable classes related to bam files. You can build yat without
    108 samtools if you run configure with `--without-samtools`, in which case
    109 bam related classes are not included in built library. Header files
    110 <sam.h> and <bam.h> are needed as well as library libbam. If you have
    111 header files available outside compiler's search path, you can help
    112 the compiler with `./configure CPPFLAGS=-I<include dir>` when header
    113 files are found in directory `<include dir>`. Likewise, you can run
    114 `./configure LDFLAGS=-L<lib dir>` when library is found in `<lib dir>`
    115 outside linker's search path. In order to run tests related to bam
    116 files, the samtools binary is also needed. If not found during
    117 configuration, these tests will be skipped. If you have samtools
    118 available outside PATH, you can help configure to find it with
    119 `./configure SAMTOOLS=/path/to/samtools`.
     104=== HTSLIB ===
     105
     106In order to enable functionality related to bam files, either htslib
     107(http://www.htslib.org) or its predecessor samtools
     108(http://samtools.sourceforge.net) must be available. Header file
     109<sam.h> is required as well as either 'libhts' or 'libbam'. The configure
     110script will try to detect whether <sam.h> is available as 'sam.h',
     111'htslib/sam.h', 'bam/sam.h', or 'samtools/sam.h'. If you have header
     112files installed outside compiler's search path, you can help the
     113compiler with `./configure CPPFLAGS=-I<include dir>` when header files
     114are found in directory `<include dir>`. Configure detects whether
     115header files are from htslib or old samtools and looks for either libhts or libbam accordingly. If library is installed outside linker's search path, in `<lib
     116dir>`, you can run `./configure LDFLAGS=-L<lib dir>`. You can build
     117yat without bam support by running `./configure --without-samtools`.
     118
     119The samtools program is needed for some tests realted to bam
     120functionality. If samtools is not found by configure, these tests will
     121be skipped. If you have samtools available outside PATH, you can help
     122configure to find it with `./configure SAMTOOLS=/path/to/samtools`.
    120123
    121124=== ZLIB ===
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