User: Click downvote

gravatar for Click downvote
Reputation:
650
Status:
Trusted
Location:
Germany
Last seen:
2 months, 4 weeks ago
Joined:
6 years, 3 months ago
Email:
e*********@gmail.com

Posts by Click downvote

<prev • 137 results • page 1 of 14 • next >
0
votes
1
answer
225
views
1
answers
Comment: C: Minimal example of using htslib from conda to build a simple c file?
... Thanks, will start to read up on it. ...
written 3 months ago by Click downvote650
0
votes
1
answer
225
views
1
answers
Comment: C: Minimal example of using htslib from conda to build a simple c file?
... It is a reimplementation of a very popular piece of software. It is already working well, I am just irked that reading bam takes 3x as long as bed reading. ...
written 3 months ago by Click downvote650
0
votes
1
answer
225
views
1
answers
Comment: C: Minimal example of using htslib from conda to build a simple c file?
... Getting the start, len, strand and reference. It is for a ChIP-Seq caller :) ...
written 3 months ago by Click downvote650
8
votes
1
answer
225
views
5 follow
1
answer
Minimal example of using htslib from conda to build a simple c file?
... This is a tiny script that is enough to get gcc to fail when trying to build: #include #include #include #include int main(int argc, char *argv[]){ samFile *fp_in = hts_open(argv[1],"r"); //open bam file bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //re ...
C conda htslib written 3 months ago by Click downvote650 • updated 3 months ago by John Marshall1.5k
0
votes
2
answers
237
views
2
answers
Comment: C: Is there a single header file somewhere I can use to read bam?
... I just need to stream the file. I guess the error is on my part as I have not used C much, just Cython. ...
written 3 months ago by Click downvote650
0
votes
2
answers
237
views
2
answers
Comment: C: Is there a single header file somewhere I can use to read bam?
... But I have the htslib conda installed and still #include errors. I think I will just use pysam, but give a warning that it is slower than the C++ bed reader. ...
written 3 months ago by Click downvote650
0
votes
2
answers
237
views
2
answers
Comment: C: Is there a single header file somewhere I can use to read bam?
... But I am using cython. How can I use compile flags to point to the system installation of htslib? Users have no way to point to an installed version when `pip installing` my library. ...
written 3 months ago by Click downvote650
2
votes
2
answers
237
views
2
answers
Answer: C: Is there a single header file somewhere I can use to read bam?
... I will submit to all of your expertise. Added htslib in a lib folder in my project. ...
written 3 months ago by Click downvote650
0
votes
2
answers
237
views
2
answers
Comment: C: Is there a single header file somewhere I can use to read bam?
... But pysam is slow as each record is a Python object which needs to be parsed. ...
written 3 months ago by Click downvote650
0
votes
2
answers
237
views
2
answers
Comment: A: Is there a single header file somewhere I can use to read bam?
... MACS2 seems to be able to read bam without any special utilities: https://github.com/taoliu/MACS/blob/33187eae605081c8ddad9313a886bd01d2c654cd/MACS2/IO/Parser.pyx#L732 However, I do not know if the code is brittle, or especially fast. It used the struct library so it cannot be compiled down to pure ...
written 3 months ago by Click downvote650

Latest awards to Click downvote

Scholar 3 months ago, created an answer that has been accepted. For C: Is there a single header file somewhere I can use to read bam?
Great Question 7 months ago, created a question with more than 5,000 views. For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question 7 months ago, created a question with more than 1,000 views. For What Are The Files Named "Random" In Genome Sequences?
Popular Question 8 months ago, created a question with more than 1,000 views. For Bioinformatics: How To Version Control Small Scripts Located All Over The Server.
Great Question 9 months ago, created a question with more than 5,000 views. For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Should You Combine Ontologies In Gohypergparams? If So, How?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Clustalw: Why Is It Bad That Many Similar Sequences Dominate The Alignment Score?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Converting Tped To Ped
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Bioinformatics: How To Version Control Small Scripts Located All Over The Server.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Representing Short Read Clusters As Feature Vectors- Which Properties To Include?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Bowtie Outputs Hits That Are Shorter Than The Reads Aligned
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Computing Similarity Between Lists Of Enriched Terms
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Creating Reads With Same Nucleotides And Dinucleotides- I.E. Scrambling Reads
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Collapse Reads That Are Substrings Of Other Reads In Same Library
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Using Bowtie To Only Search In Restricted Regions
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Where To Find Libraries/Read Files Of All Rnas Found In A Cell
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How Do I Find The Number Of Individuals In A Vcf File?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How To Tell If Bed/Bim/Fam Data Are Phased?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Data Too Big To Be Stored In Memory: Common Options

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1120 users visited in the last hour