~ubuntu-branches/ubuntu/precise/gmap/precise : revision 11

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2011-12-05 twu

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* shortread.c: Fixed bug in printing null accession for second end when

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using --fails-as-input flag

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* gmap_build.pl.in: Checking return codes from system calls

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2011-12-02 twu

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* VERSION, index.html: Updated version number

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* gsnap.c: Changed name of flag from --ambig-splice-notrim to

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--ambig-splice-noclip

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* pair.c: Pushing "0M" between adjacent I and D operations in a cigar string

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* gmap.c, gsnap.c, uniqscan.c: Using new interface to Splicetrie_setup.

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Providing --ambig-splice-notrim flag in GSNAP.

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* splicetrie.c, splicetrie.h: Providing behavior to turn clipping off at

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ambiguous known splice sites, useful if trying to turn off all soft

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clipping

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* stage1hr.c: Fixed debugging statement

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2011-11-30 twu

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* stage1.c: Fixed variable name so PMAP could compile

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2011-11-29 twu

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* dynprog.c, maxent_hr.c, maxent_hr.h, pair.c, stage1hr.c, stage3.c,

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substring.c: Checking for case where splice_pos minus margin goes beyond

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beginning of chromosome

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* VERSION, index.html: Updated version number

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* maxent_hr.c: Checking for case where splice_pos is smaller than margin

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* pair.c, samprint.c: Changed value of NM tag in SAM output to be edit

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distance (mismatches plus gaps)

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* stage1hr.c: Fixed debugging statement

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2011-11-28 twu

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* VERSION, index.html: Updated version number

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* gsnap.c: Calling SAM_setup

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* outbuffer.c: For GMAP, when quiet_if_excessive_p is true and npaths >

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maxpaths, not printing any output

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* pair.c, pair.h, stage3.c: Printing HI tag in SAM output

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* samprint.c, samprint.h: When quiet_if_excessive_p is true and npaths_mate

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> maxpaths, setting MATE_UNMAPPED in flag. Printing HI tag. Added

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function SAM_setup.

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2011-11-25 twu

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* VERSION, index.html: Updated version number

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* stage3.c: For GMAP, using QUERYEND_INDELS instead of QUERYEND_NOGAPS

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* stage1.c: Added check for querylength being too short

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* gmap.c: Changed information in --help about how to turn off chimera

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detection

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* stage3.c: In Stage3_mergeable, added check for firstpart_npairs or

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secondpart_npairs being 0

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2011-11-23 twu

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* index.html: Updated version number

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* VERSION: Updated version number

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* stage1.c: Made direct calls to fields in Match_T objects for speed. Made

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changes so debugging macros work.

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* dynprog.c: Made special traceback procedure for queryend_nogaps

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2011-11-21 twu

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* stage3hr.c: Fixed bug where Stage3end_remove_overlaps was not keeping ends

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where paired_usedp was true. In Stage3end_remove_overlaps and

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Stage3pair_remove_overlaps, terminal alignments lose to all other types.

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* stage3hr.h: Put GMAP hittype before TERMINAL hittype

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* gsnap.c: Increased default values for max_gmap_pairsearch,

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max_gmap_terminal, and max_gmap_improvement

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* stage3hr.c: Changed code for Stage3end_remove_overlaps to parallel that

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for Stage3pair_remove_overlaps

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* samprint.c: Allowing for GMAP alignments to be printed for single-end

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reads

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* VERSION, config.site.rescomp.prd, config.site.rescomp.tst: Updated version

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number

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* stage3.c: Added comment about pass 8 and 9

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* index.html: Made changes for 2011-11-20 version

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* uniqscan.c: Using new interface to Stage1_single_read

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* stage3hr.c: Changed the code for Stage3end_optimal_score to be consistent

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with that of Stage3pair_optimal_score. Allowing terminal alignments to be

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considered along with other alignments.

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* stage1hr.c: For single-end alignment, initializing done_level to

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user_maxlevel, rather than opt_level, to be consistent with the code for

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paired-end alignment. However, the values are the same anyway.

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* gsnap.c: Changed the default value for terminal_threshold from 3 to 2.

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Expanded the --help entry for --terminal-threshold.

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* index.html: Made changes for version 2011-11-17

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* stage3.c: Added more restrictions on non-canonical splices at ends of read

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2011-11-20 twu

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* stage3hr.c, stage3hr.h: Added functions Stage1end_start_endtype and

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Stage1end_end_endtype for terminal alignments

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* gsnap.c: Using new interface to Stage1_single_read

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* gmap.c, stage3.c, stage3.h: Changed name of variable

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* stage1hr.c, stage1hr.h: Implemented GMAP terminal mode for single-end

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reads

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* dynprog.c: Lowered rewards for canonical introns, to help find

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non-canonical introns

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* stage3.c: In fill_in_gaps, if splicingp is false, then filling in a

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deletion, not an intron

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2011-11-19 twu

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* stage3.c: Moved trim_noncanonical procedures from path_trim to

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path_compute. After trim_noncanonical procedures, doing an extension using

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QUERYEND_NOGAPS.

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* stage1hr.c: Using -3*nmismatches and -4 for an indel in evaluating end

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indels, corresponding to default values for trim_mismatch_score and

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trim_indel_score.

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* stage3.c: Using endalign instead of to_queryend_p. When endalign is

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QUERY_NOGAPS, not doing peelback. In pass 8, changed extendp from false

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to true (QUERYEND_INDELS).

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* gsnap.c, uniqscan.c: Added flag --trim-indel-score

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* dynprog.c, dynprog.h: Replaced to_queryend_p with endalign, with types

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BEST_LOCAL, QUERYEND_INDELS, and QUERYEND_NOGAPS. For extensions to

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queryend, always returning gappairs.

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* atoiindex.c, cmetindex.c: Updated --help to indicate how --kmer and -D are

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chosen by default

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2011-11-17 twu

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* VERSION: Updated version number

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* gmap.c, gsnap.c, stage1hr.c, stage3.c, stage3.h, uniqscan.c: Revised

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calculation of insertlength inside trim_noncanonical_ends procedures to

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compensate for using maximum overlap in computing genomicseg.

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* stage3.c: Made fill_in_gaps procedure replace short non-canonical introns

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with deletions. Removed this feature from assign_gap_types. Added

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additional checks on translation coordinates to stay within array bounds.

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* dynprog.c: Added debugging statements

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* substring.c: Added comment

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* shortread.c, shortread.h, stage1hr.c: For GMAP algorithm in GSNAP,

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assuming maximum overlap, rather than trying to compute overlap

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* outbuffer.c: Printing all paths when -E flag is given to GMAP

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* stage3hr.c: Improved error message when ambig end splicetype has an

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unexpected value

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* dynprog.c: Removed unused code for END_KNOWNSPLICING_SHORTCUT. Always

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assigning *ambig_end_length in Dynprog_end5_known and Dynprog_end3_known.

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2011-11-14 twu

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* uniqscan.c: Using new interface to Stage3hr_setup

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* stage3.c: Not substituting for long deletions at end of path_compute

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* stage1hr.c, stage3hr.c, stage3hr.h: Removed end_indel_p parameters to

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Stage3end_new_insertion and Stage3end_new_deletion

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* stage1hr.c: Preventing call to Genome_count_mismatches_limit by

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find_doublesplices where pos5 >= pos3

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* VERSION: Updated version number

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* configure.ac: Added flag --enable-popcnt

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* dynprog.c: Initialing value of ambig_end_length

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* stage3.c: Skipping gap pairs at the beginning of alignments in

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fill_in_gaps

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* goby.c: Using new interface to Result_array

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2011-11-12 twu

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* VERSION: Updated version number

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* stage1hr.c, stage3hr.c: Checking in Stage3end_new_gmap if genomicstart or

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genomicend exceeds chrhigh, and if so, returns NULL.

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* stage3.c: Moved assigning of gap types to end of path_compute, rather than

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beginning of path_trim

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* stage3.c: Inserting gap pairs and adding gap types at beginning of

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path_trim

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2011-11-11 twu

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* gsnap.c, outbuffer.c, outbuffer.h, samprint.c, samprint.h, stage1hr.c,

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stage3hr.c, stage3hr.h: Divided DISTANT_SPLICE type to SAMECHR_SPLICE and

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TRANSLOC_SPLICE. Making merge_samechr_p act only at print time, which

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allows SAMECHR_SPLICE to undergo pair_up_concordant again. Stopping

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clip-overlap on distant splices.

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* VERSION: Updated version number

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* stage3hr.c: Keeping hits in optimal scoring if nmatches_posttrim is

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sufficiently high relative to the best hit

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* gsnap.c, uniqscan.c: Increased value of max_deletionlength from 30 to 50

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* gmap.c, stage1hr.c: Using new interface to Stage3_compute

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* stage3.c, stage3.h: Changed flow to path_compute on both cdna directions,

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then pick_cdna_direction, then path_trim, which removes non-canonical end

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exons.

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* stage3hr.c, stage3hr.h, substring.c, substring.h: Added nmatches_posttrim

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and using it to break ties resulting from equal values of nmatches. Added

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a general test for Substring_new based on matches and mismatches before

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trimming.

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* pair.c: Modified Pair_nmatches to add penalties for an indel and for a

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splice site with low probabilities. Modified compute_md_string on I

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tokens to skip only for insertion pairs.

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* dynprog.c: Fixed procedure find_best_endpoint_to_queryend to look only at

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r == length1

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2011-11-10 twu

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* stage3hr.c: Turned off separate treatment of terminal alignments in

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Stage3pair_optimal_score. Always trimming ends of insertions and

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deletions (previously depended on value of end_indel_p).

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2011-11-09 twu

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* stage3.c: Using a sliding scale in trimming end exons

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* pair.c: Added debugging macro for compute_md_string

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* pair.c, pair.h: Taking cdna_direction as a parameter in

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Pair_print_exonsummary, instead of determining sense separately for each

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intron

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* stage3.c: Restored alignment score in pick_cdna_direction with different

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values of significant difference for GMAP and GSNAP. Considering a

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non-canonical intron as canonical if both splice site probabilities are

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high.

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* splicing-score.c: Fixed getopt so -D takes an argument

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* pairpool.c, pairpool.h: Revised Pairpool_count_bounded to return number of

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pairs at start.

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* gmap.c: Added comments

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* stage3.c: Restored use of alignment scores in pick_cdna_direction, after

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comparing number of noncanonical splices

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* VERSION: Updated version number

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* shortread.c: No longer printing warning message about not finding "/1" or

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"/2" endings

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* gsnap.c, uniqscan.c: Added max_deletionlength variable

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* gmap.c, outbuffer.c, outbuffer.h, pair.c, pair.h, samprint.c: No longer

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converting short noncanonical splices from type N to type D, since this is

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now performed in stage 3. Removed cigar_noncanonical_splices_p variable.

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* stage3.c, stage3.h: In assign_gap_types, converting noncanonical splices

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smaller than max_deletionlength into deletions

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* gsnap.c, stage3hr.c, stage3hr.h, uniqscan.c: Treating distant splices on

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the same chromosome as a translocation by default. Added a flag

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--merge-distant-samechr to get previous behavior.

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2011-11-08 twu

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* stage3.c: Using maxintronlen in trimming end exons

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* stage3.c: Removed alignment scores from pick_cdna_direction. Revised

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procedures for trimming noncanonical end exons and doing distal/medial

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comparison by adding procedures canonicalp and good_end_intron_p, with

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latter using probabilities.

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* gmap.c: Increased parameter for maxpeelback_distalmedial from 24 to 100

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* dynprog.c: Added debugging statements

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* pair.c: Computing MD string from cigar tokens

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* stage2.c: Restored querydist penalty

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2011-11-07 twu

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* VERSION: Revised version number

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* index.html: Added entry for new version

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* stage1hr.c: Commented out second round of terminal alignments

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* gmap.c, gsnap.c, uniqscan.c: Set trim_indel_score to -4 to be consistent

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with previous value

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* gmap.c, gsnap.c, uniqscan.c: Calling Pair_setup

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* substring.c: Extending trimming toward ends in case of ties

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* stage3.c: Extending ends completely before final trim

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* pair.h: Extending trimming toward ends in case of ties. Added Pair_setup

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function to use trim_mismatch_score value provided by user.

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* pair.c: Extending trimming toward ends in case of ties. Added Pair_setup

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function to use trim_mismatch_score value provided by user.

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* stage2.c: Put code for suboptimal starts into a compiler directive

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* gmap.c, gsnap.c, uniqscan.c: Provided new defaults for

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suboptimal_score_start and suboptimal_score_end, based on simulations

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* gmap.c, gsnap.c, stage2.c, stage2.h, uniqscan.c: Introduced parameters for

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suboptimal_score_end and suboptimal_score_start

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* gmap.c: Added flag for --suboptimal-score

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2011-11-06 twu

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* gmap.c, gsnap.c, outbuffer.c, pair.c, pair.h, result.c, result.h,

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resulthr.c, resulthr.h, samprint.c, samprint.h, stage1hr.c, stage3.c,

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stage3.h, stage3hr.c, stage3hr.h, uniqscan.c: Restoring old MAPQ score.

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Making absolute MAPQ score a separate calculation, and printing it in an

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XQ flag.

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2011-11-05 twu

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* stage1hr.c: Added comments

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* stage3hr.c: Added field indel_low, and using to prefer indels at low

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genomic coords

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* stage1hr.c: Fixed computation of firstbound and lastbound so end indels

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are found on short reads, such as 36-mers.

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2011-11-04 twu

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* pair.c: Added code to compute_cigar to merge duplicate token types

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* stage2.c: Fixed uninitialized value for last_canonicalp

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* stage2.c: Implemented ability to generate suboptimal paths based on

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different initial positions

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* gmapindex.c: Removed unnecessary file open for -P flag

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* gmapindex.c: Fixed memory leaks for -G flag

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* gmapindex.c: Fixed memory leaks for -A flag

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2011-11-01 twu

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* pairpool.c: Commented out copy of shortexonp

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* dynprog.c, dynprog.h, gmap.c, gsnap.c, stage3.c, uniqscan.c: Removed

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endlength requirement for microexons. Returning prob2 and prob3 from

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Dynprog_microexon_int and applying two standards, depending on whether an

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indel was originally present

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* pair.c: Printing shortexon information

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* pairpool.c: Copying shortexon information in copying pairs

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* smooth.c: Removed unused parameters

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* stage3.c: Adding endlength requirement for finding microexons

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* smooth.c: Printing result of smoothing as pairs

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* stage3.c: Made penalties harsher for indels at end near poor splice sites

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* stage2.c: Computing best overall score during dynamic programming process

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* uniqscan.c: Using new interface to Stage3hr_setup

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* stage2.c: Made changes so PMAP could compile

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* stage3.h: Added parameter favor_mode to Stage3_compute

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* stage3.c: Counting indel near splice as 2 mismatches. Added endlength

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requirement of 12 for indel near splice.

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* stage2.c: Going through all hits to accumulate cells. No longer using

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number of links to set root scores.

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* gmap.c, stage1hr.c: Passing value of favor_mode to Stage3_compute

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* smooth.c: Relaxing probability requirement for end exons in GSNAP from

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0.05 to 0.10.

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2011-10-31 twu

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* stage3.c: In trimming non-canonical end exons, not combining nearindelp

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with splice probs, requiring 1 mismatch or less for bingop, and allowing

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AT-AC introns. Extending alignments to queryend before trimming

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non-canonical end exons.

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* stage3.c: In trimming end exons, using a sliding scale based on intron

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length. Also penalizing for indels and mismatches close to exon-exon

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boundary.

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2011-10-28 twu

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* gsnap.c, stage1hr.c, stage1hr.h, stage3hr.c, stage3hr.h: Providing

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expected_pairlength and pairlength_deviation values in Stage3hr_setup, and

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removing from Stage1hr procedures.

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* stage3.c: In end exons, checking if indel present, and if so, requiring

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that splice probabilities both be greater than 0.9.

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* gsnap.c, stage3hr.c, stage3hr.h: Restoring pairlength deviation. Using

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expected pairlength and pairlength deviation to discriminate among

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paired-end reads.

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* stage2.c: Adding all hits from final querypos directly to celllist, rather

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than updating rootscores. Fixed update of rootscore information to use

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current querypos and hit. Dynamic programming starting from querypos 0,

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rather than querypos 1.

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* diag.c: Restricted update of diagonal in middle region, to avoid affecting

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subsequent beginning and end regions

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* splicetrie_build.c: Fixed handling of intron intervals, by introducing

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INTRON_HIGH_TO_LOW

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* stage3hr.c: Made other fixes to allow copying of GMAP hit types

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* stage1hr.c: Making copies where necessary for multiple GMAP subpaths, and

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freeing old Stage3pair_T objects at the appropriate time. Calling

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Stage3pair_remove_overlaps on double GMAP alignments.

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* pairpool.c: Using CALLOC_OUT in Pairpool_copy_array

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* gsnap.c: Printing sequence name when debugging memusage

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* stage1hr.c: Handling multiple subpaths from stage 2 computation

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* stage2.c: Removed restriction on number of positions for final non-zero

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querypos

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* stage3hr.c: Allowing Stage3end_T objects of type GMAP to be copied

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* pairpool.c, pairpool.h: Added function Pairpool_copy_array

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2011-10-27 twu

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* stage2.c: Fixed location of compiler directive for PMAP

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* stage3.c: Restoring negative points for non-canonical introns in computing

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goodness

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* stage2.c: Adding root scores for final non-zero and specific querypos

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* gmap.c, list.c, list.h, stage1hr.c, stage1hr.h, stage2.c, stage2.h: Going

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back to changes from revision 50508 for multiple subpaths from stage2,

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plus revisions 50504 to 50909 from branches/gmap-2011-10-24-mult-stage2

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for a root position method for finding optimal and suboptimal subpaths

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2011-10-26 twu

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* gmap.c, list.c, list.h, src, stage1hr.c, stage1hr.h, stage2.c, stage2.h:

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Reverted to version 50507, before changes made to allow multiple paths

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from a stage2 computation

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2011-10-24 twu

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* VERSION: Updated version number

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* archive.html, index.html: Added changes for 2011-10-24 version

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* gmap.c, list.c, list.h, stage1hr.c, stage1hr.h, stage2.c, stage2.h: Merged

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revisions 50469 to 50504 from branches/2011-10-24-mult-stage2 to allow for

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multiple stage2 results from the same genomic segment for GMAP.

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* stage3.c: Assigning sensedir in all cases, based on intron scores if

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necessary

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* gmap.c, gsnap.c, outbuffer.c, pair.c, pair.h, result.c, result.h,

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resulthr.c, resulthr.h, samprint.c, samprint.h, stage1hr.c, stage1hr.h,

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stage3hr.c, stage3hr.h, uniqscan.c: Computing MAPQ score relative to best

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alignment. Printing X2 field in SAM output to provide second best MAPQ

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score.

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* stage3.c, stage3.h: When sense_try is provided, assigning sensedir

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2011-10-17 twu

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* VERSION: Updated version number

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* index.html: Added comment about change to GMAP

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* gmap.c: Sorting stage3list before evaluating for chimeras

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2011-10-14 twu

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* VERSION: Updated version number

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* index.html: Updated for new version

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* configure.ac: Grouped together checks for built-in procedures

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* splicetrie_build.c, splicetrie_build.h: Checking for splice sites being

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beyond the chromosome length boundary

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* splicetrie.c: Handling case where trieoffsets has a NULL_POINTER, which

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can occur with intron-type splicing

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* splicetrie_build.c: Handling case where nsites from a given splice site is

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zero

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2011-10-13 twu

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* popcnt.m4: Checking each built-in instruction only if available

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* asm-bsr.m4: Assigning a value to x

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* VERSION: Updated version number

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* gsnap.c: Removed 'S' from getopt