lh3/samtools issues and pull requests

#31 - Overestimation of number of reads from nanopore data (flagstat)

Issue - State: open - Opened by rebeelouise almost 4 years ago

#30 - samtools index wheat bam

Issue - State: open - Opened by liubei8852 over 4 years ago

#29 - No base called when reference is ambiguous

Issue - State: open - Opened by snacktavish almost 6 years ago

#28 - FASTA alignment index retrieval

Issue - State: open - Opened by kullrich over 6 years ago

#27 - Small change so that the usage message displays

Pull Request - State: open - Opened by tiagomaie over 7 years ago

#26 - why we need to 'calmd' a bam file using Samtools ?

Issue - State: open - Opened by zeronot over 7 years ago

#25 - NONE

Issue - State: open - Opened by WinterLi1993 about 8 years ago - 1 comment

#24 - AD, ADR and ADF counters

Issue - State: open - Opened by iranmdl over 8 years ago

#23 - how to understand FLAG in the SAM format file.

Issue - State: closed - Opened by WinterLi1993 over 8 years ago - 2 comments

#22 - A question about samtools faidx

Issue - State: open - Opened by WinterLi1993 almost 9 years ago

#21 - Calling freeaddrinfo(NULL) results in Segmentation fault

Issue - State: closed - Opened by slowkow over 10 years ago

#20 - Argument for -m option in bcftools view when doing multi-sample variant calling

Issue - State: open - Opened by huiminkang almost 11 years ago

#19 - view -s FLOAT only works for 0.5 or below

Issue - State: open - Opened by avilella over 11 years ago - 1 comment

#18 - Can't retrieve specific region from bam built in hg19?

Issue - State: closed - Opened by xiongzhp over 11 years ago

#17 - Mpileup Issue calling indels

Issue - State: closed - Opened by colinhercus over 11 years ago - 15 comments

#16 - Adding flag to sort for giving full path to output file instead of prefix.

Pull Request - State: closed - Opened by holtgrewe over 11 years ago - 1 comment

#15 - Doesn't compile on Mountain Lion

Issue - State: closed - Opened by dawe about 12 years ago - 1 comment

#14 - add cmake support

Pull Request - State: open - Opened by domibel about 12 years ago

#13 - errmod.c ln 83 typo?

Issue - State: open - Opened by xied75 over 12 years ago

#12 - bam2bcf.c ln 57 seems redundant.

Issue - State: closed - Opened by xied75 over 12 years ago - 3 comments

#11 - 0.1.18 tag diff with sourceforge

Issue - State: closed - Opened by xied75 over 12 years ago - 2 comments

#10 - Support for retrieving type 'B' auxiliary tags

Pull Request - State: closed - Opened by nh13 over 12 years ago

#9 - Additonal SAMtools features

Pull Request - State: closed - Opened by nh13 over 12 years ago

#8 - Patches

Pull Request - State: closed - Opened by nh13 almost 13 years ago

#7 - Force standard 28 bytes empty BGZF GZIP block for no compression BAM

Pull Request - State: open - Opened by peterjc about 13 years ago - 2 comments

#6 - bam_calend should count CIGAR X/= operators

Pull Request - State: open - Opened by peterjc about 13 years ago

#5 - KNETFILE_HOOKS for using alternate network library

Pull Request - State: open - Opened by AngieHinrichs about 13 years ago

#4 - Implement basic support for =/X CIGAR operations

Pull Request - State: closed - Opened by peterjc over 13 years ago

#3 - Accept SAM files using = in CIGAR (treats X and = as M)