Module: Bio::DB::SAM::Tools

Extended by:
FFI::Library
Defined in:
lib/bio/db/sam/bam.rb,
lib/bio/db/sam/sam.rb,
lib/bio/db/sam/faidx.rb

Defined Under Namespace

Classes: Bam1CoreT, Bam1T, BamHeaderT, BamPileup1T, SamfileT, SamfileTX

Constant Summary collapse

BAM_FPAIRED = 
1
BAM_FPROPER_PAIR = 
2
BAM_FUNMAP = 
4
BAM_FMUNMAP = 
8
BAM_FREVERSE = 
16
BAM_FMREVERSE = 
32
BAM_FREAD1 = 
64
BAM_FREAD2 = 
128
BAM_FSECONDARY = 
256
BAM_FQCFAIL = 
512
BAM_FDUP = 
1024
BAM_OFDEC = 
0
BAM_OFHEX = 
1
BAM_OFSTR = 
2
BAM_DEF_MASK = 
(4|256|512|1024)
BAM_CIGAR_SHIFT = 
4
BAM_CIGAR_MASK = 
((1 << 4) -1)
BAM_CMATCH = 
0
BAM_CINS = 
1
BAM_CDEL = 
2
BAM_CREF_SKIP = 
3
BAM_CSOFT_CLIP = 
4
BAM_CHARD_CLIP = 
5
BAM_CPAD = 
6

Class Method Summary collapse

Class Method Details

.bam_sort(bam_filename, bam_output_prefix) ⇒ Object 



172
173
174
175
176
 
# File 'lib/bio/db/sam/bam.rb', line 172

def self.bam_sort(bam_filename, bam_output_prefix)
  is_by_name = 0
  max_mem = 500000000
  bam_sort_core(is_by_name, bam_filename, bam_output_prefix, max_mem)
end