https://github.com/brentp/goleft - covstats denominator

v0.2.6

covstats: fix denominator in unmapped (#73)

- Go
Published by brentp about 2 years ago

https://github.com/brentp/goleft - cram scaling

Indexcov was tuned on bam indexes. The cram (crai) indexes always looked much worse. See below for a before and after on the same data.

This required indexcov to be run with the --extranormalize flag. This is highly recommended if you are using crai files. It can clean up bam data as well. A reason to not use it would be if you want to do your own scaling/cleanup on the (more) raw data.

before: idx-indexcov-depth-chr5

after: idx-indexcov-depth-chr5-new

- Go
Published by brentp over 5 years ago

https://github.com/brentp/goleft - header fix

- Go
Published by brentp about 6 years ago

https://github.com/brentp/goleft - indexcov maintenance

v0.2.2

indexcov: better message on empty crai
indexcov: allow sending indexes as globs (to avoid argument length limit)
indexcov: if expected sex chroms are X,Y also find chrX,chrY (and use sorted order for output)

- Go
Published by brentp about 6 years ago

https://github.com/brentp/goleft - support for bai without .bams

v0.2.1

indexcov:more defense for bad crai's
indexcov: now works on just *.bai if a .fai is also given with -f.

- Go
Published by brentp about 7 years ago

https://github.com/brentp/goleft - minor bugfixes for indexcov and indexsplit

v0.2.0

indexcov: better error message and handling of excluded chromosomes.
indexcov: if given crais and no fai, indexcov will try to read the cram header using samtools view.
indexsplit: fix rare panic in CRAI files due to an off-by-one error (thanks Lavanya for reporting and providing a test-case).

- Go
Published by brentp over 7 years ago

https://github.com/brentp/goleft - crai with long reads

v0.1.19

indexcov: fix for long reads with cram. (#43)

- Go
Published by brentp almost 8 years ago

https://github.com/brentp/goleft - more cram fixes for indexcov

v0.1.18

indexsplit: fix off-by-one that resulted in double-counting some regions.
indexcov: cram edge-cases.
indexcov: better normalization to 1 for all cases. Fixes bug for bams with many (e.g. > 10K) chromosomes of which many have very low or normalization coverage. (#36)

- Go
Published by brentp almost 8 years ago

https://github.com/brentp/goleft - CRAI fixes, better sex CN counting

v0.1.17

indexcov: dont error when no sex chromosomes are found (#27).
indexcov: dont error when some chromosomes have a single region and others have 0.
indexcov: better checking on short sex chroms and other CRAI fixes.

(thanks to Javier Prado for several test-cases on CRAM)

- Go
Published by brentp over 8 years ago

https://github.com/brentp/goleft - v0.1.16

v0.1.16

indexcov: report and plot number of mapped and unmapped reads as reported by the index.
covmed: rename to covstats
covstats: report samplename(s) from read groups as well as bam path.
covstats: skip first 100K reads to give better estimates of depth.
covstats: report percent of bad (QC-Fail|Duplicate) and of umapped reads.
indexcov: automatically exclude chromosomes that match pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d$. this can be adjusted from the command-line.

- Go
Published by brentp almost 9 years ago

https://github.com/brentp/goleft - samplenames

v0.1.15

indexsplit: more closely match request number of regions.
indexsplit: allow specifying "problematic" regions which are split more finely.
samplename: new tool report the sample name of a bam from the read-group in its header.

- Go
Published by brentp almost 9 years ago

https://github.com/brentp/goleft - indexcov cram support and indexsplit

indexcov: speed and memory improvements.
indexcov: support crai.
indexcov: prettier plot and labels for pngs.
indexcov: bin plot shows proportions rather than total numbers.
indexcov: better messages and docs for --sex argument.
indexsplit: new tool to generate regions for parallelization (from bam/cram indexes) see

- Go
Published by brentp almost 9 years ago