Revision - bf57884 - Clean up many varscan modules. Rely less on samtools_path and [...] - origin: https://github.com/genome/genome

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23 March 2024, 19:04:16 UTC

Revision bf5788454706765cfd2879f14da23ca89db288d3 authored by Gabriel Sanderson on 25 March 2013, 23:58:19 UTC, committed by Gabriel Sanderson on 26 March 2013, 00:04:43 UTC

Clean up many varscan modules. Rely less on samtools_path and more on the pileup_command method.

ValidateSmallIndels -add samtools_use_baq flag to pass to varscan validation
Add a samtools_path method instead of it being a copypasted param everywhere which was confusing with samtools_version.
pileup_command_for_reference_and_bam method now takes an arrayref of bams so it can work for mpileup

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Tip revision: bf5788454706765cfd2879f14da23ca89db288d3 authored by Gabriel Sanderson on 25 March 2013, 23:58:19 UTC
Clean up many varscan modules. Rely less on samtools_path and more on the pileup_command method.

Tip revision: bf57884

File	Mode	Size
alignment_summary @ 8932081
bam-readcount @ c044123
bam-window @ 572bfaf
bassovac @ 41b7bc4
bin
breakdancer @ 8f07f3d
configuration-manager @ f719544
copyCat @ 9ab5dde
cron @ 9bb5f1f
fqgrep @ fe0206d
genome-db-cosmic @ bdec904
genome-db-omim @ d9b949a
genome-db-pfam @ e5acfb0
genome-music
genome-music-testdata @ 860ea75
genome-snapshot-deps @ be0fd25
genome-snapshot-testdata @ 72c0ded
genome-sys-user
genome-webserver
genome-www
getopt-complete @ 790cd66
gms-config @ 6ccaa62
gmt-sys-vmbuilder
graphite @ f552b86
init
jenkins @ 0d45367
joinx @ e83e763
lib
pairoscope @ 91c203a
sciClone @ d91163a
scripts
sff2fastq @ b815f97
somatic-sniper @ d736546
tgi-etc @ 08ba1a6
tigra @ 6fe6b74
tigra-sv @ 715dda8
ur @ 22f91bc
varscan @ 83ae9d8
vendor
workflow @ 7d78744
.gitignore	-rw-r--r--	93 bytes
.gitmodules	-rw-r--r--	8.8 KB
.mailmap	-rw-r--r--	301 bytes
.test-tracker.conf	-rw-r--r--	329 bytes
LICENSE	-rw-r--r--	7.5 KB
README	-rw-r--r--	154 bytes
WHERE_TO_PUT_CODE	-rw-r--r--	2.4 KB
compile_modules.t	-rw-r--r--	1.6 KB
create-c-project.sh	-rwxr-xr-x	2.9 KB
create-project	-rwxr-xr-x	2.9 KB
test-data-relocate-me	l---------	46 bytes

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https://github.com/genome/genome

Clean up many varscan modules. Rely less on samtools_path and more on the pileup_command method.

README