25 January 2013

Samtools tview as a library to display the BAM

I've forked samtools and modified the code of tview to use it as a library to display the alignments. The original code is an inreractive interface using the ncurses library. I've modified the original code and changed the structure of the C 'struct tview' with a few callbacks to make it more object-oriented:
(...)
typedef struct AbstractTview {
 int mrow, mcol;
   (...)
    khash_t(kh_rg) *rg_hash;
    /* callbacks */
    void (*my_destroy)(struct AbstractTview* );
    void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
    void (*my_mvaddch)(struct AbstractTview*,int,int,int);
    void (*my_attron)(struct AbstractTview*,int);
    void (*my_attroff)(struct AbstractTview*,int);
    void (*my_clear)(struct AbstractTview*);
    int (*my_colorpair)(struct AbstractTview*,int);
    int (*my_drawaln)(struct AbstractTview*,int,int);
    int (*my_loop)(struct AbstractTview*);
    int (*my_underline)(struct AbstractTview*);
} tview_t;
With those callbacks, there is a strong separation between the 'view' and the 'model'. Tview can now be used as a library and it's now easy to create any kind of view you need by extending the 'struct tview_t'. I've created two new interfaces: one for HTML:


samtools tview -d H examples/sorted.bam  -p seq1:20
seq1:20
 21        31        41        51        61        71        81                 
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
ATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGSTG
ATGTGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTG
ATGTGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTG
ATGTGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTG
ATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGCGCTGTGGACCCTGC       CTGTGGGGGCCGCAGTGGCTG
ATGTGTGGTTTAACTCGT     GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGCTG
ATGTGTGGTTTAACTCGT     GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGGTG
ATGTGTGGTTTAACTCGTCC   GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGCTG
ATGTGTGGTTTAACTCGTCC         CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTG
ATGTGTGGTTTAACTCGTCC         CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTG
TTTTTTGTTTTAACTCTTCTCT       CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTG
TTTTTTGTTTTAACTCTTCTCT        ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               
TTTTTTGTTTTAACTCTTCTCT        ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               
ATGTGTGGTTTAACTCGTCCATGG      ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               
ATGTGTGGTTTAACTCGTCCATGG       TTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGG              
ATGTGTGGTTTAACTCGTCCATGG       TTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGG              
ATGTGTGGTTTAACTCGTCCCTGGCCCA   TTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGG              
ATGTGTGGTTTAACTCGTCCATGGCCCAG   TAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGG            
ATGTGTGGTTTAACTCGTCCCTGGCCCA    TAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGG            
ATGTGTGGTTTAACTCGTCCATGGCCCAG   TAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGG            
ATGTGTGGTTTAACTCGTCCCTGGCCCA           CTGTGGACCCTGCAGCCTGGCTGTGGGGGGCGCCG      
ATGTGTGGTTTAACTCGTCCATGGCCCAG          CTGTGGACCCTGCAGCCTGGCTGTGGGGGGCGCCG      
ATGTGTGGTTTAACTCGTCCATTGCCCAGC         CTGTGGACCCTGCAGCCTGGCTGTGGGGGGCGCCG      
ATGTGTGGTTTAACTCGTCCATTGCCCAGC          TGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
ATGTGTGGTTTAACTCGTCCATTGCCCAGC          TGTGGACCCTGCAGCCTGGCTGGGGGGGGCGCAGT     
atgtgtggtttaactcgtccatggcccagcatt       TGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
atgtgtggtttaactcgtccatggcccagcatt       TGTGGACCCTGCAGCCTGGCTGGGGGGGGCGCAGT     
atgtgtggtttaactcgtccatggcccagcatt       TGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTTGGG   TGTGGACCCTGCAGCCTGGCTGGGGGGGGCGCAGT     
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGG    GTGGACCCTGCAGCCTGGCTGGGGGGGGCACGGGG    
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTTGGG    GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGG    GTGGACCCTGCAGCCTGGCTGGGGGGGGCACGGGG    
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTTGGG    GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
  GTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGG    GTGGACCCTGCAGCCTGGCTGGGGGGGGCACGGGG    
    GTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGC GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTG    
    GTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGC   GGACCCTGCAGCCTGGCTGTGGGGGCCGCTGTGGG  
    GTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGC   GGACCCTGCAGCCTGGCTGTGGGGGCCGCTGTGGG  
        TTTAACTCGTCCATGGCCCAGCATTAGGGATCTGT    CCTGCAGCCTGGCTGTGGGGGCCGCAGCGGGTG
        TTTAACTCGTCCATGGCCCAGCATTAGGGATCTGT    CCTGCAGCCTGGCTGTGGGGGCCGCAGCGGGTG
        TTTAACTCGTCCATGGCCCAGCATTAGGGATCTGT    CCTGCAGCCTGGCTGTGGGGGCCGCAGCGGGTG
         TTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTG      GCAGCCTGGCTGTGGGGGCCGCAGTGGCTG
         TTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTG      GCAGCCTGGCTGTGGGGGCCGCAGTGGCTG
         TTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTG      GCAGCCTGGCTGTGGGGGCCGCAGTGGCTG
           AACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGA             CTGTGGGGGCCGCAGTGGGTG
           AACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGA             CTGTGGGGGCCGCAGTGGCTG
           AACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGA             CTGTGGGGGCCGCAGTGGCTG
                 TCCATGGCCCAGCATTAGGGCGCTGTGGACCCTGC       CTGTGGGGGCCGCAGTGGGTG
                 TCCATGGCCCAGCATTAGGGCGCTGTGGACCCTGC       CTGTGGGGGCCGCAGTGGCTG
                                           GGACCCTGCAGCCTGGCTGTGGGGGCCGCTGTGGG  
                                                            TGTGGGGGCCGCAGTGGCTG
                                                            TGTGGGGGCCGCAGTGGCTG
                                                            TGTGGGGGCCGCAGTGGCTG

And another one for TEXT (with colors on a terminal):

samtools tview -d t examples/sorted.bam  -p seq1:23

        31        41        51        61        71        81        91          
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
TGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGSTGAGG
TGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTGCGG
TGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTGCGG
TGTGGTTTAACTCGTACATGGCCCAGCATTAGGGAGCTGTGGACCCCG  GCCTGGCTGTGGGGGCACCAGCCGCTGCGG
TGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGCGCTGTGGACCCTGC       CTGTGGGGGCCGCAGTGGCTGAGG
TGTGGTTTAACTCGT     GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGCTGAGG
TGTGGTTTAACTCGT     GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGGTGAGG
TGTGGTTTAACTCGTCC   GCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTG CTGTGGGGGCCGCAGTGGCTGAGG
TGTGGTTTAACTCGTCC         CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTGAGG
TGTGGTTTAACTCGTCC         CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTGAGG
TTTGTTTTAACTCTTCTCT       CATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTTG          GGCTGAGG
TTTGTTTTAACTCTTCTCT        ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               AGG
TTTGTTTTAACTCTTCTCT        ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               AGG
TGTGGTTTAACTCGTCCATGG      ATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGGGG               AGG

The code is available on github:


That's it,

Pierre


at

3 comments:

  1. AlvinWednesday, 09 October, 2013

    Awesome work! I'm trying to use tview to visualize alignments in a webpage. But I am having trouble as I am using BEDtoBam converted files, which 1) does not show the 2nd line of the viewer and 2) generates the alignments with the "." annotation.

    Is there a way to go around this and how do i default the "." toggle on/off for exporting into HTML format?

    ReplyDelete
  2. Pierre LindenbaumWednesday, 09 October, 2013

    @alvin: my code has been merged into 'samtools.0.1.19 tview'

    ReplyDelete
  3. AlvinThursday, 10 October, 2013

    Hi Pierre,

    I am aware of that and I am using version 0.1.19. I am very glad that they decided to merge your code as it is very useful. Hence I would like to know more about using it but as I am still a beginner in programming, pardon my questions.

    I am wondering how would the options such as toggle work in exporting it in html and how I could tweak it.

    Thank you

    ReplyDelete