Name	Name	Last commit message	Last commit date
Latest commit Peter Krusche Upper/lower conversion for left-alignment Feb 13, 2014 363c675 · Feb 13, 2014 History 266 Commits
lib/include	lib/include	output VCF 4.1	Feb 11, 2014
LICENSE	LICENSE	updated licensing	Oct 3, 2013
Makefile	Makefile	added profile_snps.*	Feb 11, 2014
README.md	README.md	formatting changes to look pretty from github	Dec 3, 2013
annotate_variants.cpp	annotate_variants.cpp	made coding region annotation optional	Jan 25, 2014
annotate_variants.h	annotate_variants.h	fixed abug in counting FS and NFS variants.	Jan 18, 2014
bam_ordered_reader.cpp	bam_ordered_reader.cpp	modified jump_to_interval to take in GenomeInterval instead.	Dec 13, 2013
bam_ordered_reader.h	bam_ordered_reader.h	modified jump_to_interval to take in GenomeInterval instead.	Dec 13, 2013
bcf_ordered_reader.cpp	bcf_ordered_reader.cpp	cleaned comments and formatting	Feb 6, 2014
bcf_ordered_reader.h	bcf_ordered_reader.h	modified jump_to_interval to take in GenomeInterval instead.	Dec 13, 2013
bcf_ordered_writer.cpp	bcf_ordered_writer.cpp	minor changes	Jan 7, 2014
bcf_ordered_writer.h	bcf_ordered_writer.h	minor changes	Jan 7, 2014
bcf_synced_reader.cpp	bcf_synced_reader.cpp	incportating filter into other programs plus miscelleneous changes	Feb 7, 2014
bcf_synced_reader.h	bcf_synced_reader.h	changes related to modification of BCFSyncedReader to synchronize rea…	Jan 9, 2014
compute_concordance.cpp	compute_concordance.cpp	changes related to filter rewrite	Jan 29, 2014
compute_concordance.h	compute_concordance.h	commented out i/o for the time being	Dec 3, 2013
concat.cpp	concat.cpp	added filter function for concat.	Feb 10, 2014
concat.h	concat.h	added filter function for concat.	Feb 10, 2014
construct_probes.cpp	construct_probes.cpp	removed a debug line from construct_probes.cpp	Jan 15, 2014
construct_probes.h	construct_probes.h	major overhaul of discover.cpp	Nov 25, 2013
decompose.cpp	decompose.cpp	fixed overcounting of new decomposed variants	Jan 25, 2014
decompose.h	decompose.h	added decompose.*, only site list is output even input has genotype data	Jan 25, 2014
discover.cpp	discover.cpp	fixed a memory leak	Jan 8, 2014
discover.h	discover.h	tidied view.*	Dec 3, 2013
filter.cpp	filter.cpp	incportating filter into other programs plus miscelleneous changes	Feb 7, 2014
filter.h	filter.h	incportating filter into other programs plus miscelleneous changes	Feb 7, 2014
gencode.cpp	gencode.cpp	structural codes for syn/nonsyn annotation	Feb 12, 2014
gencode.h	gencode.h	structural codes for syn/nonsyn annotation	Feb 12, 2014
genome_interval.cpp	genome_interval.cpp	added chromosify()	Jan 13, 2014
genome_interval.h	genome_interval.h	added chromosify()	Jan 13, 2014
genotype.cpp	genotype.cpp	new framework for genotyping to allow for multiple models.	Jan 15, 2014
genotype.h	genotype.h	new framework for genotyping to allow for multiple models.	Jan 15, 2014
genotyping_buffer.cpp	genotyping_buffer.cpp	added generic genotyping framwork	Jan 15, 2014
genotyping_buffer.h	genotyping_buffer.h	added generic genotyping framwork	Jan 15, 2014
genotyping_record.cpp	genotyping_record.cpp	added generic genotyping framwork	Jan 15, 2014
genotyping_record.h	genotyping_record.h	some changes.	Jan 16, 2014
hts_utils.cpp	hts_utils.cpp	changes related to incorporating bcf_has_filter()	Jan 28, 2014
hts_utils.h	hts_utils.h	changes related to incorporating bcf_has_filter()	Jan 28, 2014
index.cpp	index.cpp	index now returns an exit status of 1 when failure is encountered.	Jan 23, 2014
index.h	index.h	made changes for view and index such that it is an option to see timi…	Dec 12, 2013
interval_tree.cpp	interval_tree.cpp	privatised recursive methods of key methods.	Dec 7, 2013
interval_tree.h	interval_tree.h	changes involving GENCODE annotation in profile_snps	Jan 14, 2014
lhmm.cpp	lhmm.cpp	moved deletion and insertion check functions from genotpye.cpp to lhmm	Dec 16, 2013
lhmm.h	lhmm.h	moved deletion and insertion check functions from genotpye.cpp to lhmm	Dec 16, 2013
lhmm_genotyping_record.cpp	lhmm_genotyping_record.cpp	some changes.	Jan 16, 2014
lhmm_genotyping_record.h	lhmm_genotyping_record.h	some changes.	Jan 16, 2014
log_tool.cpp	log_tool.cpp	fixed a bug to ensure std::log10() is distinguised from LogTool.log10()	Dec 11, 2013
log_tool.h	log_tool.h	fixed a bug to ensure std::log10() is distinguised from LogTool.log10()	Dec 11, 2013
main.cpp	main.cpp	misc updates related to profile_snps	Feb 12, 2014
merge.cpp	merge.cpp	changes related to filter rewrite	Jan 29, 2014
merge.h	merge.h	changes related to merge	Jan 17, 2014
merge_candidate_variants.cpp	merge_candidate_variants.cpp	changes related to modification of BCFSyncedReader to synchronize rea…	Jan 9, 2014
merge_candidate_variants.h	merge_candidate_variants.h	miscellaneous changes.	Dec 11, 2013
merge_duplicate_variants.cpp	merge_duplicate_variants.cpp	fixed merge by position bug	Jan 24, 2014
merge_duplicate_variants.h	merge_duplicate_variants.h	renamed the i/o interface classes	Nov 18, 2013
normalize.cpp	normalize.cpp	changes to disable variant left trimming while deciding whether a var…	Jan 23, 2014
normalize.h	normalize.h	renamed the i/o interface classes	Nov 18, 2013
partition.cpp	partition.cpp	changes related to filter operations update	Feb 4, 2014
partition.h	partition.h	changes related to partition - still some logical bugs in the categor…	Jan 15, 2014
pedigree.cpp	pedigree.cpp	fixed a relationship flip bug	Jan 21, 2014
pedigree.h	pedigree.h	changes related to profiling mendelian errors	Jan 19, 2014
peek.cpp	peek.cpp	miscellaneous changes	Feb 7, 2014
peek.h	peek.h	incportating filter into other programs plus miscelleneous changes	Feb 7, 2014
profile_indels.cpp	profile_indels.cpp	misc updates related to profile_snps	Feb 12, 2014
profile_indels.h	profile_indels.h	minor changes related to profile_indels	Jan 14, 2014
profile_mendelian.cpp	profile_mendelian.cpp	changes related to filter.cpp modifications	Jan 31, 2014
profile_mendelian.h	profile_mendelian.h	related to renaming of profile_mendelian.*	Jan 29, 2014
profile_na12878.cpp	profile_na12878.cpp	misc updates related to profile_snps	Feb 12, 2014
profile_na12878.h	profile_na12878.h	added profile_na12878	Jan 29, 2014
profile_snps.cpp	profile_snps.cpp	misc updates related to profile_snps	Feb 12, 2014
profile_snps.h	profile_snps.h	added profile_snps.*	Feb 11, 2014
program.cpp	program.cpp	profile_mendelian_errors now has option to generate	Jan 29, 2014
program.h	program.h	profile_mendelian_errors now has option to generate	Jan 29, 2014
remove_overlap.cpp	remove_overlap.cpp	changes related to filter rewrite	Jan 29, 2014
remove_overlap.h	remove_overlap.h	changes related to filter rewrite	Jan 29, 2014
tbx_ordered_reader.cpp	tbx_ordered_reader.cpp	fixed a bug with file opening	Jan 10, 2014
tbx_ordered_reader.h	tbx_ordered_reader.h	changes related to profie_snps.cpp	Jan 11, 2014
utils.cpp	utils.cpp	changes related to profie_snps.cpp	Jan 11, 2014
utils.h	utils.h	changes related to profie_snps.cpp	Jan 11, 2014
variant_manip.cpp	variant_manip.cpp	Upper/lower conversion for left-alignment	Feb 13, 2014
variant_manip.h	variant_manip.h	Upper/lower conversion for left-alignment	Feb 13, 2014
view.cpp	view.cpp	added filter function for concat.	Feb 10, 2014
view.h	view.h	incportating filter into other programs plus miscelleneous changes	Feb 7, 2014

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