A text alignment viewer using the samtools API

I wrote a modified version of samtools tview. The original code uses the curses API to display an interactive sequence viewer.

I wanted to generate this kind of screen for a large number of positions and I wanted to be able to redirect the output to a unix pipeline so I changed the original code in order to only handle an extensible 2-dimensional array of characters. The code I wrote is available on github at:

https://github.com/lindenb/samtools-utilities/blob/master/src/ttview.c

.

Compilation

cd samtools/
make #compile samtools
gcc -o bamttview -g -Wall -O2 -DSTANDALONE_VERSION  -I. -Lbcftools  bam_ttview.c  bam2bcf.o   errmod.o  bam_color.o libbam.a -lbcf  -lm -lz

Example

print a position

$ ./bamttview  -g "ref:5" examples/toy.bam examples/toy.fa |\
cat -n
     1       11              21        31         41        51        61          
     2 TGTTAGATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
     3   ........    ....  ......K.K......K. ..........                                
     4   ........AGAG....***...      ,,,,,    ,,,,,,,,,                                
     5     ......GG**....AA                                                            
     6     ..C...**** ...**...>>>>>>>>>>>>>>T.....                                     

print a list of positions:

$ cat positions.txt 
ref2:10-100
ref:10-15
ref2:11

$ ./bamttview  -f positions.txt examples/toy.bam examples/toy.fa |\
cat -n | head -n 25
     1 
     2 
     3 > ref2:10-100
     4 
     5  11            21        31        41        51        61        71             
     6 aaaac****aattaagtctacagagcaactaNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
     7 ....Y    ..W...................                                                 
     8 .....****..A...                                                                 
     9 .....****..A...T.                                                               
    10 .....AAAT.............                                                          
    11 C...T****....................                                                   
    12   ..T****.....................                                                  
    13     T****......................                                                 
    14 
    15 
    16 
    17 > ref:10-15
    18 
    19  11              21        31         41        51        61        71          
    20 GATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    21 .....    ....  ......K.K......K. ..........                                     
    22 .....AGAG....***...      ,,,,,    ,,,,,,,,,                                     
    23 .....GG**....AA                                                                 
    24 .C...**** ...**...>>>>>>>>>>>>>>T.....                                          
    25 

./bamttview  -f positions.txt -d examples/toy.bam examples/toy.fa |\
cat -n | head -n 25
     1 
     2 
     3 > ref2:10-100
     4 
     5  11            21        31        41        51        61        71             
     6 aaaac****aattaagtctacagagcaactaNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
     7 ....Y    ..W...................                                                 
     8 AAAAC****AAATAA                                                                 
     9 AAAAC****AAATAATT                                                               
    10 AAAACAAATAATTAAGTCTACA                                                          
    11 CAAAT****AATTAAGTCTACAGAGCAAC                                                   
    12   AAT****AATTAAGTCTACAGAGCAACT                                                  
    13     T****AATTAAGTCTACAGAGCAACTA                                                 
    14 
    15 
    16 
    17 > ref:10-15
    18 
    19  11              21        31         41        51        61        71          
    20 GATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    21 .....    ....  ......K.K......K. ..........                                     
    22 GATAAAGAGGATA***CTG      taggc    cagcgccat                                     
    23 GATAAGG**GATAAA                                                                 
    24 GCTAA**** ATA**GCT>>>>>>>>>>>>>>TTCAGC                                          
    25 

That's it,

Pierre