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Maxcompute #1

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Maxcompute #1

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ShujiaHuang
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lyman and others added 30 commits July 10, 2017 20:02
@lyman
external table extractor for oss mpileup/samplename files
da8a9e9
@lyman
add README
a2d50d2 
Change-Id: I03fdb11c992970830f13cc7e75983ba869b1e713
@lyman
udf to expand oss external table into one wide table
cf5c543 
Change-Id: I59a7f58436fb03b76b403f350a3fe54650e0c903
@lyman
update README
d28f26f 
Change-Id: I46084b5b5f5d710787e3249ec5a9343ae63e1647
@lyman
BaseVar coverage udf
9ec92e4 
Change-Id: Id23a304b32b676145d162f03f0a34e628c8dfb48
@lyman
basevar vcf part basically done
25e8599 
Change-Id: I43aba2128f1edc8ad4cdd88210316b21d1dc62d7
@lyman
refine code format
42264a5 
Change-Id: I773b407110b05c687bf6dbb1a4935bf06f9ff80d
@lyman
deal with 'N ! .' properly, add local run, enable scan_indel
82fb933 
Change-Id: I6db62e175ca154216c5e3f9344f4ca05cb678ebc
@lyman
fix coverage break, update README
05cfd44 
Change-Id: I27cc10c700f63f8b1c72e7017df09036e0375d17
@lyman
workaround for jdk bug http://bugs.java.com/view_bug.do?bug_id=7021870
60ad66a
@lyman
fix sample count not match in wide table
375e2e8 
Change-Id: I08a10b99d91d75b4cbf97909352bacac59541df1
@lyman
performance optimize: list.append -> fixed length list + index access
e4fa912 
Change-Id: I1b67496ec9f3406f4c5385adc4229e9068173de3
@lyman
update README
c70bd2e 
Change-Id: I9dc991b55f64a10b1a665f8dc5eef57ff71b0ff0
@lyman
add zh_cn README
646470c
@tianliplus
[OSS Table] ignore '0 * *'
ed58250 
Change-Id: I27d9f51e6388aa0032ade0975ae92d29a9766d1e
@ShujiaHuang
New function for derectory dealing with bam/cram files instead of mpi…
da816de 
…leup
@ShujiaHuang
pep8 stype
93be5ff
@ShujiaHuang
delete some un-necesry function
d4e4303
@ShujiaHuang
small modify
3590fb4
@ShujiaHuang
add coverage function
47a0add
@ShujiaHuang
add coverage function
1c4800e
@ShujiaHuang
use prop.trend.test to calculate the different of north, central and …
59d9eea 
…south
@tianliplus
Merge branch 'baminput' into maxcompute
b7a09a3
@ShujiaHuang
re-use the scipy to do statistic test
ff5b553
@tianliplus
Merge branch 'develop' into maxcompute
10e95e3
@tianliplus
fix conflict
650460d 
Change-Id: I258ed09865d3b3625b55b2c4374fcd515524358f
@ShujiaHuang
split('\t') -> split()
7b05d97
@tianliplus
add pileup to process
cd130ce 
Change-Id: Ia9ac55fe4af99c0459cd05cf6104649e9fa806a2
@ShujiaHuang
add some log information when processing the basetype
99fdd8f
@ShujiaHuang
log of loading sample's id
06e6136
ShujiaHuang and others added 30 commits February 12, 2018 09:10
@ShujiaHuang
fix bugs
746a12e
@tianliplus
add basevar doc
b5b28c6 
Change-Id: Ia2c520a70a0d0777f7ddc67eaf99740511a0b0e2
@tianliplus
add new py file
185ef6c 
Change-Id: I7cdf58acfcb1d1d996e12bffd76804f1b4972551
@ShujiaHuang
modify the expression logist of EM algorithm, exchange the E-STEP and…
63f7d13 
… M-STEP and update many others
@ShujiaHuang
delete some redundancy code when we use pysam.AlignmentFile to open a…
c9822a6 
…lignment files
@ShujiaHuang
A module to create fusion file(something like g.vcf) for large cohort…
170be2a 
… projects
@ShujiaHuang
fix bugs
d463fb6
@ShujiaHuang
delete one blank line
5e7edc5
@ShujiaHuang
'!'->base_qual
9624c2f
@ShujiaHuang
do not need go_iter to track the iteration of bamfile and delete some…
f73fc9f 
… useless code, make the program more clear
@ShujiaHuang
sooner or later I'll delete this py code
3b1d693
@ShujiaHuang
set the threshold of MAF to be smaller
90ce320
@ShujiaHuang
change the log information
88f045b
@ShujiaHuang
commit the basetype process from fusion files
bfbc7b1
@ShujiaHuang
improve the quality for mono-allelic
7d8e603
@ShujiaHuang
samll modify
d09ad8c
@ShujiaHuang
input regions could be a file or just like chr:start-end
9753072
@ShujiaHuang
N+1 problem and calculate the allele frequence for different populati…
9f830d0 
…on group
@ShujiaHuang
For N+1 testing
0280139
@ShujiaHuang
add testing data for N+1
0c232a4
@ShujiaHuang
how to download the reference
1313697
@tianliplus
Merge branch 'gvcf' into maxcompute
375b88c
@tianliplus
[Basevar] popgroup
556f0be 
Change-Id: Ide68fff8b589898b4b6e7142069f3ee1afe01b72
@tianliplus
[MaxCompute] 14w_test code done
5a62b1b 
Change-Id: I7071bd475a54e9b2e3a881200323b8f57f8f81f1
@tianliplus
multiple shard
fb78b52 
Change-Id: I235185a981ed21d3f9e3d499f5fe03433a60bf57
@tianliplus
fix oom caused by dynamic partition
dcb1a88 
Change-Id: Ib2c8b0e5b399f4424fb13cc634bacd6fc1a84b5b
@tianliplus
external table support shard and method partition
450233e 
Change-Id: I1397d48339f4bdb8e016fb9dbe8db70e9c82254b
@tianliplus
add oss-input
85c5e0d 
Change-Id: Iea527fb0074d40b030f44a2b2e745a6e34f52b33
@tianliplus
add gene-ibs
1d42334 
Change-Id: Iae26baaf26bbe73f57ae2d8bc8bd38424f9b4a38
@tianliplus
fix buffer
0a890f5 
Change-Id: I132295c87b412a5b9f9c3ede8f67719c12b515b6
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3 participants
@ShujiaHuang @lyman @tianliplus