a5912cdbd4
move all hight throughput sequencing stuff to hts namespace
4 years ago
74f94c4778
add etc directory
4 years ago
7deab8abd4
backup the old directory and module structure
4 years ago
0570f76f4d
added the bio.std.experimental directory. Moved new bio2 to experimental
4 years ago
0bac2ffd5f
move fasta and fastq modules to bio.std.file
4 years ago
dbfc47339d
move decompress.d module to core
4 years ago
ae3a9263a4
rearrange directories
4 years ago
2196f29f54
Merge branch 'master' of github.com:biod/BioD
4 years ago
baaefefdd0
GzipbyLine: pass line counter
4 years ago
7f5277f3df
README build instructions with dub and meson
4 years ago
3627559ded
use explicit import messages. comment sections to allow for debugging
4 years ago
25068c1c43
size_t is uint on 32-bits platform. Fixes #43 . Thanks @tillea .
4 years ago
d2d2ac9b47
Updated dub.json
4 years ago
1828b14d7c
Merge branch 'master' of github.com:biod/BioD
4 years ago
ac5725a19d
GzipbyLineThreaded: multi-threaded vesion uses mmfile
4 years ago
fb0aca9912
GzipbyLine: fix last empty line
4 years ago
dd48716948
make use of explit module import for learning purposes
4 years ago
84d14e6014
SimpleSplitConv: strtok replacement
4 years ago
e3e18530c4
GzipbyLine: implementation
4 years ago
01891fff60
Decompress: add test file
4 years ago
c7e2ec0ddd
Decompress: started work on GzipbyLine
4 years ago
4f1a7d2fb7
Merge pull request #42 from TimurIs/master
Comparator for query name sort as in Picard
4 years ago
b96eafa930
adding new comparator for string/bam_read
4 years ago
8453e40c27
adding new comparator
4 years ago
332b06114e
Merge pull request #40 from george-githinji/master
fixed deprecation warnings while running the benchmark
4 years ago
1856f72f6b
Fixed deprecation warnings by making use std.datetime.stopwatch.StopWatch for running the benchmark
4 years ago
da7045e408
cleanup
4 years ago
0e8ed55683
Use std.datetime.stopwatch.StopWatch
4 years ago
33fc2401d6
Merge pull request #39 from george-githinji/master
remove a recursive import
4 years ago
5d54ecd6f0
Merge branch 'master' of github.com:biod/BioD
4 years ago
5a1e131e44
ignore the dub.selections.json
4 years ago
fc7bf3641a
removed recursive import
4 years ago
9a23d27d17
Merge pull request #38 from ximion/master
Update Meson build, fix tests - thanks @ximion
4 years ago
c059165f35
meson: Modernize Meson build definition
4 years ago
ee9428fea0
meson: Include bio2 in libbiod build
4 years ago
643b454f04
trivial: Fix unittests
4 years ago
0243e7590b
Release 0.2.1
4 years ago
2f0634b187
Fix BioD/bio/maf/reader.d(41): Deprecation: struct `std.stdio.File.ByLine!(char, char).ByLine` is deprecated - Use .byLine
4 years ago
87dcc1af5a
Fixes https://github.com/biod/BioD/issues/37
4 years ago
92afd2d14a
Merge branch 'master' of https://github.com/biod/BioD
4 years ago
11a569f51e
Add PM header to be in line with samtools
Fixes https://github.com/biod/sambamba/issues/356
4 years ago
877283225e
Fix link in RELEASE-NOTES
4 years ago
df33db0880
-a
VERSION file added
4 years ago
ff04629e86
Changelog
4 years ago
c865ee2de2
Compilation fixes for ldc 1.11
4 years ago
dd07f34979
Fixes:
BioD/bio/maf/reader.d(53): Error: cannot implicitly convert expression `this._f.byLine(cast(Flag)true, '\x0a')` of type `ByLineImpl!(char, char)` to `ByLine!(char, char)`
See https://github.com/bioconda/bioconda-recipes/pull/8787#issuecomment-389195848
4 years ago
3513df92a6
update github account link
4 years ago
8527852a38
README
4 years ago
f4a6c1c55c
Introducing my recent D-style rewrite of bamreader. This version is still
single threaded (there is room for pre-fetching blocks), but proves very fast
and lazy.
The original working commits can be found on this branch
https://github.com/pjotrp/sambamba/tree/markdup2
4 years ago
a84bbed78f
Merge branch 'master' of github.com:pjotrp/BioD
4 years ago
George Githinji