Changeset 3364

Nov 25, 2014, 2:17:50 PM (8 years ago)

describe htslib support in NEWS and README. refs #794

2 edited


  • 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)
    1011  A complete list of closed tickets can be found here [[br]]
  • trunk/README

    r3114 r3364  
    102102== Optional packages ==
    104 === Samtools ===
    106 Samtools available from 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 ===
     106In order to enable functionality related to bam files, either htslib
     107( or its predecessor samtools
     108( 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`.
     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`.
    121124=== ZLIB ===
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