df4cd3b86a
Adding support for building sharedlibrary in make file
3 years ago
d2cb603b56
Bringing unittests back in
3 years ago
c3c2a81839
fix the module imports for test
4 years ago
7deab8abd4
backup the old directory and module structure
4 years ago
643b454f04
trivial: Fix unittests
4 years ago
bfeef2bfa8
Getting rid of unittest noise
5 years ago
576c0793bf
All unittest output on stderr
5 years ago
c37b0e7e03
switch to undead.stream;
6 years ago
93ac39e25b
fix compression buffer size
7 years ago
2765f2f5d1
fixes here and there
8 years ago
f88fe6479d
fix unittests to compile with LDC
9 years ago
1560f69119
faster BAM reading
9 years ago
52d0ae3ce7
better SAM parser
9 years ago
57c81f275f
changed license to MIT
9 years ago
32fb5a45a4
new BamRead method: extended_cigar
(CIGAR with =/X instead of M -- requires MD tag)
9 years ago
73da46c93e
new awesome serialization to sam/json
10 years ago
2ecabe69c5
fixes in Value.toString
10 years ago
bf12b493f4
implemented idiomatic toString for BamRead
Other improvements:
* _is_slice is now hackishly contained in the chunk
(name is zero terminated, so one byte is available)
* Each BamRead now contains a pointer to the reader
* SamReader and BamReader now share common interface
bio.bam.abstractreader.IBamSamReader
10 years ago
81909e480c
unittests pass on 2.061
10 years ago
7bd9a276a0
added PerBaseInfo.constructFront method
10 years ago
61e9ae13c1
split mdExtra into mdCurrentOp, mdNextOp, mdPreviousOp
10 years ago
7847d19753
added Option.mdExtra to basesWith
* that allows to get previous, current, and next MD operation for
each base
10 years ago
aaddb9333c
support for options in basesWith
Currently, only one option is supported, which provides
cigar_after and cigar_before properties for each PerBaseInfo.
10 years ago
852c1b62e6
fixed unittests by adding opEquals to PerBaseInfo.Result
10 years ago
8907b118ed
renamed module pileuprange to pileup
10 years ago
ec2c9aeb0c
basesWith: MD tag
10 years ago
f4984db147
renames: writeRead -> writeRecord; phred_base_quality -> base_qualities
10 years ago
2fadd7f1ff
new BamWriter class; bio.bam.output is deprecated
10 years ago
d38d2b17da
bgzf input/output streams
10 years ago
9218e12a38
moved BGZF-related code to bio.core.bgzf
10 years ago
5ef136fc9d
renamed read_name to name
10 years ago
ec3dc0986b
changes in basesWith behaviour
10 years ago
c37567fee0
renamed Sam/BamFile to Sam/BamReader and made them classes
10 years ago
da9824be96
make unittests compile with -property
10 years ago
a1dcb7075e
initial commit
10 years ago
Pjotr Prins