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Commits : Listings

Analyzed 1 day ago. based on code collected 1 day ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Jan 28, 2025 — Jan 28, 2026 Showing page 123 of 136 Search / Filter on:
[no comment]	pd3	More...				over 16 years ago
implemented version() for the mappers	sb10	More...				over 16 years ago
[no comment]	pd3	More...				over 16 years ago
for reads pairs where both are unmapped, include the mate_unmapped flag, like bwa does it	sb10	More...				over 16 years ago
changed mapping quality determination by setting minimum 0 for repetative reads	sb10	More...				over 16 years ago
new Math utils module	sb10	More...				over 16 years ago
reimplemented flag output in cigar_to_sam() to fix bugs; now outputs unmapped reads as well	sb10	More...				over 16 years ago
added new calculate_flags() method	sb10	More...				over 16 years ago
made %flags our instead of my	sb10	More...				over 16 years ago
[no comment]	tk2	More...				over 16 years ago
sam_to_fixed_sorted_bam now takes a ref.fa so it can run fillmd	sb10	More...				over 16 years ago
avoid uninitialized value warning	sb10	More...				over 16 years ago
added dict file location to lane_info	sb10	More...				over 16 years ago
changed sam_to_fixed_sorted_bam so that it also runs the bam via fillmd; fixed add_sam_header to put in correct md5s	sb10	More...				over 16 years ago
changed sam_to_fixed_sorted_bam so that it also runs the bam via fillmd; fixed add_sam_header to put in correct md5s	sb10	More...				over 16 years ago
file changed, do not remember why or how	sb10	More...				over 16 years ago
safer line check	sb10	More...				over 16 years ago
new dict parser	sb10	More...				over 16 years ago
[no comment]	tk2	More...				over 16 years ago
[no comment]	tk2	More...				over 16 years ago
added GenomeAnalysisTK resource files, including the analyze script	sb10	More...				over 16 years ago
removed ancient broad recal files	sb10	More...				over 16 years ago
upgrading to latest samtools with NM-calculating fillmd support	sb10	More...				over 16 years ago
latest and greatest version	sb10	More...				over 16 years ago
[no comment]	pd3	More...				over 16 years ago
add_sam_header now adds RG tags to records	sb10	More...				over 16 years ago
trivial addition of explanatory comments	sb10	More...				over 16 years ago
tests for merge_and_check added	sb10	More...				over 16 years ago
read_group passed to do_mapping; split-level merge done with samtools, since picard fucks up the RG tags	sb10	More...				over 16 years ago
new read_group arg for do_mapping; further improvements to avoid repeating mapping when files already present	sb10	More...				over 16 years ago

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