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 |