Changeset 3363


Ignore:
Timestamp:
Nov 25, 2014, 11:42:54 AM (8 years ago)
Author:
Peter
Message:

improve docs. refs #794

Location:
trunk/yat/omic
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/yat/omic/BamFile.h

    r3357 r3363  
    8686
    8787#ifndef YAT_HAVE_HTSLIB
    88     /// Old samtools 0.1.xx had a struct samfile_t, which in htslib has
    89     /// changed to samFile
     88    /**
     89       \brief only defined when compiling against old bamlib
     90
     91       Old samtools 0.1.xx had a struct samfile_t, which in htslib has
     92       changed to samFile
     93    */
    9094    typedef samfile_t samFile;
    9195#endif
     
    122126       libbam, \c bam_index_t.
    123127
    124        \see index(void)
     128       \since New in yat 0.13
     129
     130       \see function index(void) const
    125131     */
    126132#if YAT_HAVE_HTSLIB
     
    183189       \brief read the next BamRead
    184190
     191       This function is used in BamReadIterator. Typically it is more
     192       convenient to read bams via a BamReadIterator than through this
     193       function directly.
     194
    185195       \return true on success
    186196     */
     
    252262       \param compression a number [0,9] indicating level of
    253263       compression. 9 gives highest compression and 0 indicates no
    254        compression (suitable for piping between applications)
     264       compression (suitable for piping between applications).
    255265
    256266       \since yat 0.12
  • trunk/yat/omic/BamHeader.h

    r3352 r3363  
    8282       \brief inverse of target_name(size_t)
    8383
    84        \note If \a name does not exist, behaviour is undefined.
     84       If compiled against libbam and \a name does not exist,
     85       behavious is undefined. If compiled against htslib, a
     86       utility::runtime_error is thrown.
    8587
    8688       \since new in yat 0.11
     
    8991
    9092    /**
    91        Number of chromosomes
     93       \return Number of chromosomes
    9294     */
    9395    int32_t n_targets(void) const;
  • trunk/yat/omic/BamReadFilter.h

    r3361 r3363  
    2828#include <functional>
    2929
     30// this flag was defined in bam.h but has disappeared in htslib
    3031#ifndef BAM_DEF_MASK
    3132#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
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