BamDeal | BamDeal : a comprehensive toolkit for bam manipulation
kandi X-RAY | BamDeal Summary
kandi X-RAY | BamDeal Summary
BamDeal is a C++ library. BamDeal has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.
soap --> bam/sam Format. bam/sam --> soap Format. bam/sam --> Fastq Format. bam/sam --> Fasta Format. filter low quality read in bam. split single/muti-Bam by chr. split single/muti-Bam by assign chr. Merge/Cat diff header muti bam to one bam. random out partly of bam read. get/remove some chr form bam. modify seq phred quality in bam. Limit big bam to muti subbam by fix line. Calculate Genome Coverage/Depth/GC Dis based Bam (v1.32). Calculate Genome every Site's four base Depth. Detect CNV/Deletion Region by merge Depth info based Bam. Detect SV by Pair End Read insert size in Bam. GiveOut bed file of low Depth Region(may BigDeletion). Basic Stat and qualty control,Show gc-depth... result Fig. Show pdf Fig of Depth Dis & Depth~Coverage. Show pdf Fig of Depth~RefGC. Show Manhattan Fig of Depth sliding Windows along genome.
soap --> bam/sam Format. bam/sam --> soap Format. bam/sam --> Fastq Format. bam/sam --> Fasta Format. filter low quality read in bam. split single/muti-Bam by chr. split single/muti-Bam by assign chr. Merge/Cat diff header muti bam to one bam. random out partly of bam read. get/remove some chr form bam. modify seq phred quality in bam. Limit big bam to muti subbam by fix line. Calculate Genome Coverage/Depth/GC Dis based Bam (v1.32). Calculate Genome every Site's four base Depth. Detect CNV/Deletion Region by merge Depth info based Bam. Detect SV by Pair End Read insert size in Bam. GiveOut bed file of low Depth Region(may BigDeletion). Basic Stat and qualty control,Show gc-depth... result Fig. Show pdf Fig of Depth Dis & Depth~Coverage. Show pdf Fig of Depth~RefGC. Show Manhattan Fig of Depth sliding Windows along genome.
Support
Quality
Security
License
Reuse
Support
BamDeal has a low active ecosystem.
It has 47 star(s) with 19 fork(s). There are 4 watchers for this library.
It had no major release in the last 12 months.
There are 2 open issues and 1 have been closed. On average issues are closed in 384 days. There are 1 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of BamDeal is v0.27
Quality
BamDeal has 0 bugs and 0 code smells.
Security
BamDeal has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
BamDeal code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
BamDeal is licensed under the MIT License. This license is Permissive.
Permissive licenses have the least restrictions, and you can use them in most projects.
Reuse
BamDeal releases are available to install and integrate.
Installation instructions, examples and code snippets are available.
Top functions reviewed by kandi - BETA
kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of BamDeal
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of BamDeal
BamDeal Key Features
No Key Features are available at this moment for BamDeal.
BamDeal Examples and Code Snippets
No Code Snippets are available at this moment for BamDeal.
Community Discussions
No Community Discussions are available at this moment for BamDeal.Refer to stack overflow page for discussions.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install BamDeal
Download For linux/Unix static you can use the statically compiled programs directly. For linux/Unix and macOS compile Pre-installations of 4 libraries or softs are required before installing BamDeal 1 htslib: samtools-1.9/htslib-1.9 1.5 <= htslib <= 1.9 2 g++ : g++ with --std=c++11 > 4.8+ is recommended 3 zlib : zlib > 1.2.3 is recommended 4 R : R with ggplot is recommended. Note1: If fail in [./configure], to find library htslib, you can add LDFLAGS to find the htslib library and CXXFLAGS and CFLAGS to find the htslib header [ ./configure LDFLAGS=-L/usr/lib/ CXXFLAGS=-I/usr/include/ CFLAGS=-I/usr/include/]; export 'LIBRARY/CFLAGS/CXXFLAGS' environment variables to set the htslib path also can be a way to compile, such : export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH;. Note2: you can use the statically compiled programs directly [chmod 755 ./bin/BamDeal_Linux; ./bin/BamDeal_Linux].
To compile BamDeal, do [ ./configure] first, then [make]
Final software can be found in the direcoty [bin/BamDeal]
To compile BamDeal, do [ ./configure] first, then [make]
Final software can be found in the direcoty [bin/BamDeal]
Support
For any new features, suggestions and bugs create an issue on GitHub.
If you have any questions check and ask questions on community page Stack Overflow .
Find more information at:
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
