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biopieces.git
2008-12-05
martinahansen
fixed CHR_BEG=0 bug
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2008-12-05
martinahansen
changed barray from ushort to uint
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2008-12-05
martinahansen
added bed2tag_contigs as backend to assemble_tag_contigs
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2008-12-05
martinahansen
added bed2tag_contigs.c
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2008-12-05
martinahansen
added bed2fixedstep.c as backend to calc_fixedstep
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2008-12-05
martinahansen
fixed bed2fixedstep.c
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2008-12-04
martinahansen
added python code
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2008-12-04
martinahansen
added bed2fixedstep.c
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2008-11-30
martinahansen
added barray.c and cleaned hash.c
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2008-11-28
martinahansen
removed GIW2008 poster to docs and added to featured...
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2008-11-28
martinahansen
added GIW2008 poster to docs
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2008-11-27
martinahansen
added c power to calc_fixedstep
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2008-11-24
martinahansen
fixed bugs in calc_fixedstep
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2008-11-24
martinahansen
fixed bugs in assemble_tag_contigs
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2008-11-24
martinahansen
major code upgrade 1
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2008-11-21
martinahansen
fixed bug in compute
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2008-11-18
martinahansen
doc update
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2008-11-18
martinahansen
clean up
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2008-11-13
martinahansen
added -c switch to write_bed
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2008-11-11
martinahansen
added ucscMakeTracks -b run to remove_ucsc_tracks
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2008-11-11
martinahansen
finished remove_ucsc_tracks
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2008-11-11
martinahansen
fix date and time in ucsc config
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2008-11-11
martinahansen
added remove_ucsc_tracks
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2008-11-11
martinahansen
added -t to remove_mysql_tables
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2008-11-11
martinahansen
swapped bedSort with bed_sort
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2008-11-11
martinahansen
added mysql related Biopieces
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2008-11-07
martinahansen
finished assemble_tag_contigs
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2008-11-03
martinahansen
rewrote grab to get speed
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2008-10-28
martinahansen
fixed compute
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2008-10-28
martinahansen
fixed bug in compute and analyze_seq
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2008-10-27
martinahansen
changed delimiter in REC_TYPE SOLID to ;
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2008-10-02
martinahansen
added REC_TYPE to read_solid
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2008-09-29
martinahansen
empty change to Seq.pm
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2008-09-29
martinahansen
tada
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2008-09-25
martinahansen
fixed ugly bug
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2008-09-25
martinahansen
fixed rename bug
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2008-09-24
martinahansen
adding rescan to bipartite_scan
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2008-09-23
martinahansen
fixed STDERR and verbose
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2008-09-23
martinahansen
add bipartite_decode
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2008-09-23
martinahansen
add bipartite_decode
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2008-09-23
martinahansen
backup time
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2008-09-17
martinahansen
added SPAN to read_psl
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2008-09-17
martinahansen
fixed tmp dir cleaner in Biopieces.pm
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2008-09-16
martinahansen
added 5prime adaptor feature to remove_adaptor
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2008-09-16
martinahansen
inline::c code for adaptor removal
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2008-09-16
martinahansen
minor updates
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2008-09-11
martinahansen
bed_sort created
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2008-09-11
martinahansen
added bed stuff to c code
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2008-09-10
martinahansen
added copyright to c stuff
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2008-09-10
martinahansen
bipartite_scan polish2
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2008-09-10
martinahansen
linked list sort added
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2008-09-10
martinahansen
bipartite_scan polish
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2008-09-08
martinahansen
fixed 0 offset bug in remove_adaptor
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2008-09-08
martinahansen
added sort to bipartite_scan.c
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2008-09-05
martinahansen
bipartite_scan now working
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2008-09-05
martinahansen
added c temp file dir
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2008-09-05
martinahansen
added unit test to mem.c
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2008-09-04
martinahansen
bipartite_scan.c alpha
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2008-09-03
martinahansen
removed wiggle options from upload_to_ucsc
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2008-09-03
martinahansen
fixed -S and -L for calc_fixedstep biopiece
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2008-09-03
martinahansen
added calc_fixedstep biopiece
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2008-09-01
martinahansen
read_solexa now handles both decimal and octal scores
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2008-08-29
martinahansen
fixed bug in remove_adaptor
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2008-08-29
martinahansen
fixed minor bugs in remove_adaptor
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2008-08-29
martinahansen
added remove_adaptor biopiece
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2008-08-29
martinahansen
added remove_adaptor biopiece
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2008-08-29
martinahansen
fixed UCSC::get_psl_entry
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2008-08-28
martinahansen
fix of \r feature in Fasta::get_entry
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2008-08-28
martinahansen
read_fasta fix for stupid \r
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2008-08-26
martinahansen
fixed bug in table name check
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2008-08-26
martinahansen
made speedup for repeat-O-matic
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2008-08-26
martinahansen
added fixedStep format to upload_to_ucsc
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2008-08-25
martinahansen
clean-write of repeat-O-matic
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2008-08-25
martinahansen
added --verbose run option for blast_seq
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2008-08-25
martinahansen
added revcomp_dna to repeat-O-matic
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2008-08-22
martinahansen
fixed read_soft to deal with stupid Soft format feature
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2008-08-22
martinahansen
added option to read_soft for selecting specific samples
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2008-08-21
martinahansen
finished c fasta parser
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2008-08-21
martinahansen
finished c fasta parser
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2008-08-21
martinahansen
fixed format_genome
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2008-08-21
martinahansen
fixed bug in vmatch_index
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2008-08-21
martinahansen
fixed %d->%f for log10 in upload_to_ucsc
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2008-08-21
martinahansen
more updates of c and fixes to upload_to_ucsc
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2008-08-18
martinahansen
another c code upgrade
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2008-08-14
martinahansen
updated read_solexa
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2008-08-14
martinahansen
unit test of mem.c done
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2008-08-13
martinahansen
update of c libs
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2008-08-05
martinahansen
fixing up c code
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2008-08-01
martinahansen
changed result key of count_records
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2008-07-29
martinahansen
reverted code for format_genome in order to make vmatch...
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2008-07-29
martinahansen
correcting bug in Match.pm
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2008-07-29
martinahansen
finished biopiece merge_records
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2008-07-28
martinahansen
added new biopiece merge_records
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2008-07-25
martinahansen
fixed zero entry tmp file bug in soap_seq
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2008-07-25
martinahansen
fixed another annoying bug in clean_tmp()
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2008-07-25
martinahansen
corrected bug in clean tmp to deal with permision problem
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2008-07-25
martinahansen
changed error output to fit on screen
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2008-07-24
martinahansen
added seed_size to soap_seq
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2008-07-24
martinahansen
corrected ugly bug
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2008-07-24
martinahansen
fixed cleanup of temporary files
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