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ChangeLog
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2012-06-02 twu
* genome.c: Added assertions to Genome_get_char and Genome_get_char_blocks
to check for negative coordinates
* dynprog.c: Removed debugging statements
* stage3.c: Fixed get_genomic_nt to check for both genomicpos between 0 and
genomiclength, and pos between chroffset and chrhigh
* dynprog.c: Fixed get_genomic_nt to check for both genomicpos between 0 and
genomiclength, and pos between chroffset and chrhigh
* VERSION, index.html: Updated version number
* dynprog.c, stage3.c: Checking only for genomepos < 0 in get_genomic_nt,
not for chrpos between chroffset and chrhigh, which may need further
debugging for chimeras.
* dynprog.c: Checking for genomepos < 0 in get_genomic_nt.
* stage3.c: For Stage3_extend_left and Stage3_extend_right, using
get_genomic_nt instead of going directly to Genome_get_char. Checking for
genomepos < 0 in get_genomic_nt.
* stage3hr.c: In Stage3pair_remove_overlaps, allowing separate pair to
subsume overlapping pair only if it is better
2012-06-01 twu
* stage3.c: Fixed check of chrpos to compare genomicpos against chrhigh
* dynprog.c: Fixed check of chrpos to compare genomicpos against chrhigh
* dynprog.c, stage3.c: Checking for chrpos between 0 and chrhigh - 1,
inclusive
* dynprog.c, dynprog.h, gmap.c, gregion.c, gregion.h, splicetrie.c,
splicetrie.h, stage1hr.c, stage3.c, stage3.h: Passing chrhigh along with
chroffset to all procedures
* dynprog.c, genome.c: When chromosomal coordinate is negative, returns '*'
instead of 'N'. Traceback procedures in dynamic programming will not add
pairs with '*' genomic nucleotides.
* util: Merged changes from last branch
* config.site.rescomp.tst: Updated version number
* README: Added note that MAX_READLENGTH applies only to GSNAP
* VERSION, index.html: Updated version number
* stage2.c, stage3.c: Merged changes from
branches/2012-06-01-merge-single-gap to fix problems with merging single
gap on minus strand
2012-05-31 twu
* stage3.c: Protected another debugging statement from referring to
genomicseg
* gsnap.c: Fixed documentation for --fails-as-input flag.
* gmap.c: Added --fails-as-input string to getopt processing. Fixed
documentation for --fails-as-input flag.
* dynprog.c: Added messages to stderr before all abort statements
* translation.c: Requiring translation_leftpos and translation_rightpos to
be between 0 and querylength-1.
2012-05-25 twu
* gmap_build.pl.in: If -k 15 specified, but not -b, setting basesize to be
12
* Makefile.gsnaptoo.am: Added uniqscan program
* stage1hr.c: Decreased max_nalignments from 3 to 2
* dynprog.c: For known splicesites, adjusted low and high boundaries so
contlength is always between 0 and endlength-1, inclusive.
* stage3.c: Not reducing genomejump at ends anymore
2012-05-23 twu
* VERSION, index.html: Updated version number
* gmap.c, stage1hr.c: Increased max_nalignments for stage 2 to 3
* stage3hr.c: Turned off check for cdna_direction != 0 and SENSE_NULL in
declaring a GMAP alignment as bad
* stage3.c: Changed pass 9 from queryend_indels to queryend_nogaps, to avoid
false positive indels at ends and to prepare for noncanonical end trimming
* splicetrie.c: Improved debugging statements
* pair.c: Added information about knowngapp and protectedp in printing pair
information for debugging purposes
* stage3.c: In trimming of noncanonical introns near end, making an
exception for known introns
* dynprog.c: Replaced noindel version of Dynprog_end_splicejunction
functions with version allowing indels
* stage3.c, stage3.h, stage3hr.c: In Stage3_bad_stretch_p, excluding trimmed
regions on ends
* uniqscan.c: Using new interfaces to setup procedures
* stage1hr.c: Added debugging statements
* genome_hr.c: Removed debugging statements
* gamma-speed-test.c: Using new interface to setup procedures
* dynprog.c, dynprog.h, stage3.c: Introduced new endalign type,
QUERYEND_GAP, and using it in pass 8. Restored call of Dynprog_end
procedures in trim ends using BEST_LOCAL, which does not try to find an
intron.
* stage3.c: Better handling of ends: pass 8, best_local plus known splicing;
pass 9, queryend_indels; pass 10, queryend_nogaps. Medial gap not using
known splicing. Simplified trim_ends procedure. Not removing or
re-inserting known intron gaps. Bayesian computation of mapping scores
for GMAP alignments.
* splicetrie.c: Computing separate offsets for anchor and far splicesites
for use in Dynprog_end_splicejunction procedures. Not calling
Dynprog_add_known_splice procedures.
* pairdef.h, pairpool.c, pairpool.h: Added knowngapp field to Pair_T object
* dynprog.c, dynprog.h: Allowing compute_scores procedures to work on
genomicseg (for splicejunctions). Added functions
Dynprog_end5_splicejunction and Dynprog_end3_splicejunction to replace
add_known_splice procedures. Calling traceback_local_nogaps in two parts.
Dynprog_end_gap procedures returning final score even for QUERYEND_INDELS.
Made debugging statements work without genomicseg.
2012-05-21 twu
* samprint.c: Checking if MD string output is empty and if so printing "0"
2012-05-19 twu
* stage3hr.c: For paired-end reads, in cases of tie score, sorting results
by genomic position
2012-05-18 twu
* splicetrie_build.c: For intron-level splicing information, sorting
individual splicesites by ascending genomic position
* splicetrie.c, splicetrie.h: Computing spliceoffset needed to construct
splicejunctions. Calling Dynprog_local_nogaps procedures. Requiring
dynprog score > 0 on known splicejunctions.
* dynprog.c, dynprog.h: Fixed bug in making A-G and C-T ambiguous scores for
all modes. Implemented traceback procedure using given sequence and no
gaps for handling known splicejunctions. End dynamic programming
procedure now returns a final score for queryend_nogaps endalign.
Implemented make_contjunction procedures to retrieve the continuous part
of splicejunctions. Made make_splicejunction_3 consistent with
make_contjunction_3.
* stage3hr.c: Turned off check for min_splice_prob on GMAP alignments, since
it appears not to work for known splicesites
* pair.c: Pair_dump_list now prints line to indicate start of list
2012-05-17 twu
* dynprog.c: Handling cases where length1 == 0 or length2 == 0, which
otherwise cause fatal errors
* stage3.c: Setting use_genomicseg_p to false in all cases
* stage2.c: Using Oligoindex_hr_tally even if user genomic segment provided
* gmap.c: Computing genomicend even if user genomic segment provided
* genome-write.c: Added extra 4 words to end of genome blocks to accommodate
nextlow in Oligoindex_hr procedures
* Makefile.gsnaptoo.am: Added source files for GMAP
2012-05-16 twu
* VERSION, config.site.rescomp.prd, config.site.rescomp.tst, index.html:
Updated version number
* stage1.c, stage1.h: Added procedure for nonstranded alignment. Turning
off scan_ends algorithm and using only sampling. Using indexdb size limit
for standard mode, but not for cmet-nonstranded mode.
* stage2.c: Looking up genomic nt for all alignment pairs in
convert_to_nucleotides
* uniqscan.c: Using new interfaces to setup routines
* gsnap.c: Using new interfaces to setup routines
* gmap.c: Using different indexdb size thresholds for standard and
cmet-nonstranded modes
* stage1hr.c: Using new interfaces to stage 2 procedures
* stage3.c, stage3.h: Handling AMBIGUOUS_COMP the same as MATCH_COMP and
DYNPROG_MATCH_COMP. Removed genomic_offset argument from Stage2_compute.
Fixed intermediate alignment results for debugging by returning pairs
instead of path from path_compute.
* oligoindex_hr.c, oligoindex_hr.h: Fixed Cmet_reduce commands for
CMET_STRANDED mode
* match.c: Fixed memory leak in a debugging procedure, Match_print
* gregion.c, gregion.h: Made Gregion_filter_support function available
again. Added function Gregion_genestrand.
* Makefile.dna.am, dynprog.c, dynprog.h, genome.c, genome.h, gmap.c,
stage2.c, stage2.h: Added code to make GMAP work on cmet-stranded and
cmet-nonstranded modes
2012-05-14 twu
* stage3hr.c: Disallowing new Stage3pair_T object if its insertlength
exceeds pairmax and we expect a concordant pair
* Makefile.dna.am, block.c, block.h, boyer-moore.c, boyer-moore.h,
config.site.rescomp.tst, dynprog.c, dynprog.h, genome-write.c,
genome-write.h, genome.c, genome.h, genome_hr.c, genome_hr.h, gmap.c,
gsnap.c, intlist.c, intlist.h, oligoindex.c, oligoindex.h,
oligoindex_hr.c, oligoindex_hr.h, pair.c, pair.h, splicetrie.c, src,
stage1.c, stage1.h, stage1hr.c, stage2.c, stage2.h, stage3.c, stage3.h,
stage3hr.c, stage3hr.h, trunk, uniqscan.c, util: Merged revisions 63606 to
64016 from branches/2012-05-08-genomic-nts to read genomic nt rather than
generate genomicseg
2012-05-11 twu
* archive.html, config.site.rescomp.tst, dynprog.c, index.html, src, trunk,
util: Merged revisions 63773 through 63823 from
branches/2012-05-10-better-affine-gap to make score matrix symmetric, put
sequence2 in outer loop, fix boundary conditions, and improve efficiency
* resulthr.c: Fixed uninitialized value for X2 on halfmapping_mult
alignments
* samprint.c: Fixed uninitialized value for X2 on halfmapping_uniq
alignments
2012-05-08 twu
* gtf_genes.pl.in, gtf_introns.pl.in, gtf_splicesites.pl.in: Made -E flag
use exon_number field
* gtf_genes.pl.in, gtf_introns.pl.in, gtf_splicesites.pl.in: Added -E flag
to ignore exon_number fields in GTF file
2012-05-07 twu
* VERSION: Updated version
* oligoindex_hr.c: Reverting to version that zeroes out counts for oligomers
that are overabundant or not in query
* gmap.c, stage1hr.c, stage2.c, stage2.h: Providing a limit on the number of
suboptimal alignments returned from stage 2. Limit set to 2 for GMAP and
1 for GSNAP.
* gsnap.c: Added getopt handler for --sam-multiple-primaries
2012-05-03 twu
* VERSION, config.site.rescomp.tst, dynprog.c, gmap.c, pair.c, pair.h, src,
stage1hr.c, stage3.c, stage3.h, stage3hr.c, stage3hr.h, trunk, util:
Merged revisions 63036 to 63240 from branchese/2012-05-01-affine-gap to
implement an affine gap algorithm for dynamic programming
* uniqscan.c: Using new interface to Stage1hr procedure that contains
first_absmq as an argument
* shortread.c: Generalized handling of old Illumina paired-end format ending
in :0 or :<digit>.
* genome.c: Fixed function Genome_fill_buffer_simple_alt so it returns
ref+alt, instead of empty+alt.
* indexdb.c: Made writing of offsetscomp file faster when blocksize == 1 (or
k == b), by using a single write command instead of looping.
* goby.c, outbuffer.c: Implemented patches for Goby 2.0
* gmap.c, gsnap.c, outbuffer.c, pair.c, pair.h, result.c, result.h,
resulthr.c, resulthr.h, samprint.c, samprint.h, stage1hr.c, stage1hr.h,
stage3.c, stage3.h, stage3hr.c, stage3hr.h: Added flag
--sam-multiple-primaries to allow multiple alignments to be marked as
primary, if their mapping scores are equally good
* shortread.c: Handling older style Illumina paired-end reads that end in
":0"
* stage3.c: Fixed debugging statements
* oligoindex_hr.c: Not zeroing out counts[i] for oligomers that are either
overabundant or not in query. Saves time in allocate_positions function
and in store functions.
2012-04-28 twu
* VERSION, config.site.rescomp.prd, config.site.rescomp.tst, index.html:
Updated version
* gmap.c: Using new interface to Stage3_compute
* stage3hr.c, stage3hr.h: Using nmatches_posttrim (adjusted by scores for
indels) to compare alignments, except for pre-final terminals. Performing
iteration in optimal_score procedures to use updated trim boundaries as
poor alignments are removed.
* stage3.h: No longer use nmatches_pretrim in Stage3_compute
* stage3.c: Removed use of QUERYEND_INDELS at ends of reads, and using
QUERYEND_NOGAPS instead, to reduce time spent in dynamic programming
* stage1hr.c: Added usedp field to Segment_T object, and marking it true if
the segment is used in making a Stage3end_T object. Skipping these
segments in finding terminals.
* pair.c, pair.h: Added pos5 and pos3 arguments to Pair_nmatches
* genome.c: Made uncompress_mmap faster by translating high and low words 16
bits at a time. Adding N's only if flags is not zero.
* dynprog.c: Modified bridge_intron_gap so it searches for indels on left or
right of splice, but not both. Changes algorithm from quadratic to linear
time.
2012-04-25 twu
* stage1hr.c, stage3hr.c, stage3hr.h: Revisions made to hit_goodness_cmp and
hitpair_goodness_cmp. Using genomiclength in hit_goodness_cmp, final
round. For terminals, returning 0 in preliminary rounds. Not using
scores for terminals, and using scores only if GMAP or indels are
involved. In pair_up procedure, not using terminal scores to update
found_score.
* indexdb.c: Fixed uninitialized variables that caused problems with older
GMAP indices
2012-04-23 twu
* dynprog.c: Created separate functions, compute_scores_lookup_fwd and
compute_scores_lookup_rev
* splicetrie.c: Fixed calls to Dynprog_end5_gap and Dynprog_end3_gap to use
endalign instead of to_queryend_p.
2012-04-20 twu
* VERSION: Updated version
* stage3hr.c: Added check for too many indel breaks in GMAP
* stage1hr.c, stage3hr.c, stage3hr.h: Storing cdna_direction in hit of type
GMAP and using it instead of sensedir when printing
2012-04-19 twu
* VERSION, index.html: Updated version number
* stage3.c: Turned off debugging
* stage3.c: Fixed uninitialized variable in trim_novel_spliceends
* dynprog.c, dynprog.h, stage3.c: Using correct endalign types in
Dynprog_end5_known and Dynprog_end3_known
* pair.c: Fixed issue with uninitialized variable in printing splicesite
labels
2012-04-18 twu
* result.c, result.h: Added mergedp variable
* outbuffer.c, outbuffer.h: Handling results where mergedp is true
* gmap.c: Allowing chimera finding to be turned off by setting -x to be 0.
Added mergedp variable so merged alignments generate only a single result.
2012-04-16 twu
* VERSION, config.site.rescomp.tst, index.html: Updated version
* samprint.c: Handling case where clip-overlap results in a NULL substring
* gmap.c: In call to Stage3_merge_local_single, clipping parts around
breakpoint instead of chimerapos and chimeraequivpos, to avoid issues
where maxpeelback is insufficient
* stage3.c, stage3.h: Renamed variable from extendp to max_extend_p
* get-genome.c: Added --forsam flag to generate header for SAM files
2012-04-11 twu
* VERSION: Updated version
* stage1hr.c: Fixed bug from uninitialized variable
* gmap.c, stage3.c, stage3.h: Added a criterion for extending left and right
chimera ends to consecutive mismatches, based on queryjump and genomejump
being unequal.
2012-04-09 twu
* gsnap.c, uniqscan.c: Using new interface to Stage3hr_setup
* stage1hr.c: Finding terminals by a new method. Instead of counting
mismatches from end, requiring only that querypos3 - querypos5 is greater
than index1part. Now searching terminals on single-end reads even if a
GSNAP alignment has been found. Removed nsalvage == 0 requirement for
searching terminals and paired-end reads.
* substring.c, substring.h: Added procedure Substring_set_endtypes
* stage3hr.c, stage3hr.h: Changed optimal score procedures to use max of
max-terminal and min-other for prefinal rounds, and max of max-GMAP and
min-other for final rounds. For GMAP eventrim scores, not counting
indels, and adding a penalty for long ambiguous ends, by dividing by
index1part + (index1interval - 1). Terminal alignments now compute their
own endtypes.
2012-04-06 twu
* stage2.c: Fixed fatal bug when looking for shifted canonical splice site
by checking that rightpos is less than genomicend.
* gmap.c, stage3.c, stage3.h: For chimeras, extending ends until three
consecutive mismatches are found. At final breakpoint, cleaning indels
from ends.
2012-04-05 twu
* stage1hr.c: For single-end reads, finding distant splicing only when no
other hits have been found
* VERSION, index.html: Updated version
* pair.c, pair.h, stage3.c: Fixed bug in Stage3_mergeable where we require
end1 and start2 pairs to be computed
2012-04-04 twu
* index.html: Updated version
* VERSION: Updated version
* splicetrie.c: Allowing 1 mismatch in distal exon
* stage3hr.c: Changed debugging statement to report score_eventrim
* stage3.c: Rewrite trim_novel_spliceends to scan pairs first to find
genomicpos bounds and then iterate through genomicpos. Allowing
pick_cdna_direction to return SENSE_NULL if no introns exist.
* stage1hr.c: For GMAP terminals, also checking for a bad stretch in GMAP
result after the call to align_halfmapping_with_gmap
* stage3.c: Fixed bug in trim_novel_spliceends when pairs is NULL
* stage3.c: Turned off trimming of novel splice ends for GMAP
* index.html: Made changes to reflect new version
2012-04-03 twu
* VERSION: Updated version
* stage3hr.c: Fixed issue where no non-terminal alignment existed, resulting
in using min trim length of MAX_READLENGTH
* splicetrie.c: Allowing only 1 mismatch (previously 2) in internal splice
region of 6 bp, and no mismatches in external splice region (previously
depended on extension). This avoids bad splicing due to poor gene models.
* pair.c, pair.h, stage3.c: Using pairs instead of pairarray in determining
whether chimera ends are connectable
* pair.c, pair.h, stage3hr.c: Counting indels in GMAP alignments only within
eventrim region
* stage3.c: Added function trim_novel_spliceends
* pair.c: Requiring that cdna_direction not be zero when printing splice
site probabilities at the ends
2012-04-02 twu
* VERSION, chimera.c, chimera.h, gmap.c, outbuffer.c, pair.c, pair.h,
pairpool.c, pairpool.h, src, stage1hr.c, stage3.c, stage3.h, stage3hr.c,
stage3hr.h, trunk, util: Merged revisions 60621 to 60936 from
branches/2012-03-27-gmap-chimeras to improve GMAP chimeras and to apply a
uniform eventrim procedure in stage 3 optimal score procedures
2012-03-30 twu
* gamma-speed-test.c: Added to SVN repository
* atoiindex.c, cmetindex.c, config.site.rescomp.tst, configure.ac, gmap.c,
gsnap.c, indexdb.c, memory-check.pl, pdldata.c, snpindex.c: Added
--enable-mmap flag to configure. Added small fixes to allow programs to
work without mmap.
* stage3hr.c: Allowing trimming on both ends of a terminal alignment
* pair.c: Handling case where hard clipping is not possible
2012-03-27 twu
* stage1hr.c: Handling the case where GMAP alignment is attempted on a
translocation
2012-03-23 twu
* VERSION, index.html: Updated version
* stage1hr.c: Added multiple checks for GMAP bad stretch
2012-03-22 twu
* index.html: Updated for latest version
* stage1hr.c: Fixing fatal bug when max_end_insertions is set to less than 3
2012-03-21 twu
* VERSION: Updated version
* index.html: Updated for new version
* gsnap.c: Reduced default value of distant-splice-penalty from 2 to 1
* gsnap.c: Reduced default value of distant-splice-penalty from 3 to 2
* stage1hr.c: Changed criterion for GMAP salvage from
Stage3end_bad_stretch_p to Stage3end_score > cutoff_level, because
previous criterion caused GSNAP to miss distant splicing
* archive.html: Updated for new version
* index.html: Updated for new version
* dbsnp_iit.pl.in: Checking whether the exceptions field is defined in the
snp file
2012-03-20 twu
* gmap.c, outbuffer.c, stage3.c, stage3.h: Removed some unused parameters
* VERSION: Updated version
* stage3hr.c: Changed score for GMAP alignments to be post-trim matches
minus penalties for splicing and indels. Allowing Stage3end_bad_stretch_p
to handle GMAP alignments.
* stage3.c: Not doing any peelback on the extension after trim_ends
* stage1hr.c: Moved check for GMAP bad stretch from elimination as a very
bad alignment to a salvage status
* dynprog.h: Added comment
2012-03-19 twu
* pair.c, pair.h, stage3.c: Added an extend step after the ends are trimmed,
to get as long an extension as possible.
* stage1hr.c, stage3.c, stage3.h: Added a check for GMAP alignment length,
in addition to the bad stretch check
* gmap.c: Using new interface to Stage3_compute
* substring.c: Added comment
* stage1hr.c, stage3.c, stage3.h, stage3hr.c, stage3hr.h: Removed
computation of gmap_nconsecutive, and implemented Stage3_bad_stretch_p to
evaluate GMAP alignments instead.
2012-03-16 twu
* gff3_genes.pl.in, gff3_introns.pl.in, gff3_splicesites.pl.in: Filtering
out comment lines beginning with '#'.
* gff3_genes.pl.in, gff3_introns.pl.in, gff3_splicesites.pl.in: Printing
results for last mRNA in each gene
2012-03-15 twu
* stage3.c: In traversing dual break, accepting the stage 2 solution only if
the entire query sequence is bridged
* gff3_genes.pl.in, gff3_introns.pl.in, gff3_splicesites.pl.in,
gtf_genes.pl.in, gtf_introns.pl.in, gtf_splicesites.pl.in: Made gff3 and
gtf programs handle exons in arbitrary order
* gtf_genes.pl.in, gtf_introns.pl.in: Checking for comment lines
* gtf_genes.pl.in, gtf_introns.pl.in: Allowing GTF file to lack exon_number
field
* gtf_genes.pl.in: Checking both gene_name and gene_id to get gene name
2012-03-13 twu
* gmap.c, inbuffer.c, inbuffer.h: Added -1 flag for self-align feature
2012-03-12 twu
* configure.ac: Changed default value of MAX_READLENGTH from 200 to 250
* README, config.site: Changed default value of MAX_READLENGTH from 200 to
250
* stage1hr.c: Added missing else statement
* dynprog.c, splicetrie.c, splicetrie.h: Changed Splicetrie_solve_end5 and
Splicetrie_solve_end3 to take triecontents, trieoffsets, and j, rather
than triestart, and to check for a null pointer.
* stage3hr.c: No longer returning NULL from Stage3end_new_gmap when result
crosses before beginning of genome or at end of chromosome.
* stage1hr.c: Removed possibility of dereferencing uninitialized memory when
skipping over diagonals straddling beginning of genome.
2012-03-09 twu
* gmap.c, stage3.c, stage3.h: Made changes in Stage3_merge_single compatible
with PMAP
* Makefile.dna.am, gsnap_fasta.c: Moved gsnap_fasta.c and bam_fasta and
sam_fasta programs to GSTRUCT repository
* get-genome.c: Fixed -E option for printing exons from gene map files.
Added -S option for printing sequence from gene map files.
* get-genome.c: Removed R from getopt string
* get-genome.c: Removed -R flag and references to map_relativep
2012-03-08 twu
* gmap.c: Removed debugging statement
* gmap.c: Fixed test for CHIMERA_SLOP to handle minus strand alignments
correctly. Added a remove duplicates step to stage3list_from_gregions.
Using new interface to Stage3_merge_single and Stage3_merge_splice.
* stage3.c, stage3.h: Implemented functions Stage3_merge_single and
Stage3_merge_splice. The first function uses dynamic programming to solve
the region between the two parts.
* pair.c, pair.h: Implemented function Pair_set_genomepos_list
2012-03-07 twu
* gsnap.c: Fixed default values in --help statement for number of GMAP runs
allowed
* stage1hr.c: Turned bad stretchp back on as a criterion for running GMAP
improvement in paired-end reads. Implemented GMAP improvement for
single-end reads.
* substring.c, substring.h: Implemented Substring_genestrand
* stage3hr.c, stage3hr.h: Added genestrand as a field for Stage3end_T object
2012-03-02 twu
* stage3.c: Added another check to make sure we don't try to solve for dual
breaks at the ends of an alignment
2012-03-01 twu
* dynprog.c: Making certain that left_prob and right_prob are initialized to
0.0
* splicetrie_build.c: Limiting distance for splicetries to shortsplicedist
* stage3.c: Checking for endgappairs == NULL, before trying to access
*endgappairs
2012-02-29 twu
* configure.ac: Changed default .config.site to ./config.site
* dynprog.c: Fixed cases where left_prob and right_prob were not assigned
* stage3.c: Making singlep a local variable in traverse_dual_genome_gap
* stage3.c: Setting *singlep to false to fix bug in traversing dual genome
gaps where left goodness or right goodness was called after a dual gap
win.
2012-02-28 twu
* gmap.c: Calling Alphabet_setup, Oligo_setup, Oligop_setup, Indexdb_setup,
and Stage1_setup only when genome is provided
* gmap.c, stage3.c, stage3.h: Restored cdna_direction == 0 when no splices
are present. Transferring overall cdna_direction to first Stage3_T object
in a chimera.
2012-02-27 twu
* stage3.c: Disallowing cdna_direction to be set to 0
* gmap.c: Added call to Oligo_setup
* indexdb.c: Looking for offsetscomp_suffix exactly
* gmap.c: Using new interface to Stage3_compute
2012-02-24 twu
* VERSION: Updated version number
* stage3.c: Handling case where non-canonical splice is exactly in the
middle of the read
* stage1hr.c, stage3.c, stage3.h, stage3hr.c, stage3hr.h: Replaced
high_quality computation on gmap alignments with gmap_nconsecutive
* outbuffer.c: Implemented new Goby code
* gsnap.c: Implemented new Goby code
* goby.c, goby.h: Implemented new Goby code
* gtf_splicesites.pl.in: Skipping comment lines that begin with '#'.
* gtf_splicesites.pl.in: Removed requirement for exon_number field in GTF
file
* gmap_build.pl.in: Added -T flag to specify temporary build directory
* gmap_build.pl.in: Deleting .coords file
2012-02-14 twu
* gmap_build.pl.in: Fixed filenames for 1-digit values
* oligo.c: Added repetitive oligos for 6-, 7-, and 8-mers.
* indexdb.c: Improved warning message
* gmap_build.pl.in: Made default value for base size to be kmer size
* configure.ac: Moved read of config.site and setting of CFLAGS earlier, so
default CFLAGS is not set by autoconf.
* setup1.test.in: Changed name of positions file to reflect new naming
scheme
* README: Added comment about new naming for positions file
* Makefile.am, setup.ref12123positions.ok, setup.ref123positions.ok: Changed
name of positions file to reflect new naming scheme
* VERSION: Updated version
* config.site.rescomp.prd, config.site.rescomp.tst: Changed dates
* configure.ac: Adding check for CFLAGS and setting default to be -O3
* config.site: Commenting out default CFLAGS variable
* README: Added comment about adding -m64 in CFLAGS for Macintosh machines
* gsnap.c, stage1hr.c, stage1hr.h: Added control of gmap_indel_knownsplice
feature to gsnap program
* stage3hr.c, stage3hr.h: Added function to help run GMAP on indels to find
known splicing
* stage1hr.c: Added function to run GMAP on indels to find known splicing
* stage1.c: Using new interface to Reader_new
* pmapindex.c: Removed -R flag for processing reverse strand of genome.
Consolidated code for computing offsets and positions.
* pair.c: Eliminated extra points subtracted from Pair_nmatches, so that the
function reports the correct number of matches
* dynprog.c: Fixed bug where known splicing was being called when length2
was 0, resulting in bad endpoints for binary search
2012-02-03 twu
* stage1hr.c: Using spansize in computing floors. Reduced value of
STAGE2_MIN_OLIGO from 5 to 3.
* gsnap.c: Using new interface to Stage1hr_setup and Spanningelt_setup
* uniqscan.c: Using new interface to Stage1hr_setup and Spanningelt_setup
* reader.c, reader.h: Removed blocksize as a field for Reader_T object
* oligo.c, oligo.h: Storing oligosize as a static variable, and not using it
anymore as a parameter to Oligo_next or Oligo_skip.
* block.c: Removed oligosize as a field from Block_T object
* stage1hr.c, stage3hr.c, stage3hr.h, substring.c, substring.h: Revised
Stage3end_optimal_score to compare terminal and non-terminal alignments
using an eventrim procedure, based on the maximal trims found in the
non-terminal alignments, and re-computing the mismatch scores in those
regions.
* stage1hr.c: Running Stage3end_remove_overlaps to remove terminals that
overlap with a GSNAP alignment. Using spansize to compute fast_level.
Removed index1part (oligosize) from calls to Reader_new and Oligo_next.
* stage1hr.c, stage1hr.h: Generalized from 6 to STAGE2_MIN_OLIGO +
index1interval, for deciding whether a found diagonal is close enough to
end to redefine region for GMAP alignment. Using spansize to compute
floors, and counting all mismatches if spansize != index1part.
* spanningelt.c, spanningelt.h: Added function Spanningelt_setup, which
computes spansize for a given index1part and index1interval
2012-02-02 twu
* pairdef.h, pairpool.c, stage3.c: Added field end_intron_p to Pair_T
object, and using it in traversing dual genome gaps. When applicable,
solving introns where left intron or right intron is omitted.
* stage1hr.c: Improved debugging messages by printing chromosomal
coordinates rather than universal coordinates
* Makefile.dna.am, atoiindex.c, cmetindex.c, config.site.rescomp.prd,
config.site.rescomp.tst, genomicpos.c, genomicpos.h, gmap_build.pl.in,
gmap_setup.pl.in, gmapindex.c, indexdb.c, indexdb_hr.c, memory-check.pl,
pmapindex.c, snpindex.c, spanningelt.c, spanningelt.h, src, stage1hr.c,
trunk, types.h, util: Merged revisions 56772 to 56962 from
branches/2012-01-31-index1interval to allow genomic indices up to 16-mers
and sampling intervals from 1 to 3
2012-02-01 twu
* resulthr.c, stage3hr.c, stage3hr.h: If anomalous splices (of type
SAMECHR_SPLICE) occur within a read for a unique mapping, changing
resulttype from _UNIQ to _TRANSLOC.
* outbuffer.c: Fixed issue with double opening of nomapping output file,
first as single and then as paired
2012-01-31 twu
* gmapindex.c: Allowing only values 1, 2, and 3 for sampling interval
* gmap.c, gsnap.c, indexdb.c, indexdb.h, stage1hr.c, stage1hr.h, uniqscan.c:
Added --sampling flag and passing index1interval to Stage1hr_setup
* uniqscan.c: Using new interface to Indexdb_new_genome
* indexdb.c: Fixed incorrect variable name (oligo instead of oligoi).
* gmap_build.pl.in: Removed fixed value of -q 3 in calls to gmapindex
2012-01-30 twu
* gmap_build.pl.in: Added -q flag for sampling interval
* gmap.c, gmapindex.c, gsnap.c: Allowing user to enter -k 16
* block.c, indexdb_dump.c, indexdb_hr.c, stage1.c, stage1hr.c: Fixed mask
calculation to use unsigned long, so kmer of 16 works
* atoiindex.c, cmetindex.c, indexdb.c, indexdb.h, snpindex.c: Enabled
writing of genome indices with kmer of 16
* oligo.c: Allowing k-mer size of 16
* genome_hr.c: Clarified types of gamma and value to be Positionsptr_T and
firstbit to be int.
2012-01-27 twu
* oligo.c: Allowing k-mer size to go down to 9
* indexdb_hr.c, indexdbdef.h: Eliminated separate data storage for offsets
when expand_offsets_p is true. Instead, expanding gammas into offsetscomp
and making gammaptrs just the identity function.
* indexdb.c: Eliminated separate data storage for offsets when
expand_offsets_p is true. Instead, expanding gammas into offsetscomp and
making gammaptrs just the identity function.
2012-01-19 twu
* indexdb.c, indexdb.h: Allowing selection of base size, and returning found
base size. Simplified logic for selecting indexdb.
* gmap.c, gsnap.c: Added --basesize flag to allow user to select base size
* gmapindex.c: Allowing k-mer size to be 15 or less
2012-01-18 twu
* gmapindex.c: Added break after handling flag -b
2012-01-14 twu
* VERSION: Updated version number
* Makefile.three.am: Rebuilt instructions from Makefile.gsnaptoo.am, plus
Makefile.dna.am for PMAP and PMAPINDEX
* Makefile.gsnaptoo.am: Removed gsnap_tally from distribution
* README: Change URL for Web site
* alphabet.c: No longer checking new get_codon procedures against old ones
* pmapindex.c: Revised limit for 8-mers to be alphabet size of 13 or less
* README.PMAP: Added a README file for PMAP
2012-01-13 twu
* indexdb.c, indexdb.h: Providing alphabet and alphabet_size to caller of
Indexdb_new_genome
* gmap.c: Added --alphabet flag to PMAP to specify a particular alphabet
* atoiindex.c, cmetindex.c, genome_hr.h, snpindex.c, types.h: Moved
definition of Storedoligomer_T from indexdbdef.h to types.h
* block.c, block.h, stage1.c: Removed msb computation and storage in Block_T
object, and initializing instead by Oligop_setup
* alphabet.c, alphabet.h, oligop.c, oligop.h: Providing aa_index_table to
Oligop procedures at run time
* Makefile.dna.am, alphabet.c, alphabet.h, indexdb.c, indexdb.h,
indexdbdef.h, pmapindex.c: Created Alphabet_T object. Moved relevant
codon-based procedures from indexdb.c to alphabet.c. Replaced
get_codon_fwd and get_codon_rev with lookup tables. Allowed pmapindex to
generate indices with different alphabets and alphabet sizes.
* gmapindex.c: Added check for k-mer size being greater than or equal to
base size
* gmap.c: Made default k-mer size 7 for PMAP
* Makefile.dna.am, indexdb.c, pmapindex.c: Made PMAP index files compatible
with compressed hash tables and added flags to be consistent with other
auxiliary indexing programs
2012-01-11 twu
* VERSION: Updated version
* index.html: Updated Web page for latest version
* mapq.c: Fixed debugging statement
* stage3hr.c: In output_cmp procedures, sorting first by nmatches (pretrim),
and then by mapq. Added procedure to enforce monotonicity of mapq scores.
* stage1hr.c, stage3hr.c, stage3hr.h: Running optimal_score first allowing
all GMAP alignments, then removing overlaps, and then running
optimal_score again without special provision for GMAP alignments.
* gmap.c, gsnap.c, pair.c, pair.h, uniqscan.c: Added flag --sam-use-0M to
control printing of 0M in CIGAR strings
* gmap.c, gsnap.c, stage3.h, uniqscan.c: Providing output_sam_p to
Stage3_setup
* stage3.c: In fill_in_gaps, handling dual breaks by inserting query and
genomic segments when output_sam_p is true.
* pair.c: In compute_md_string, setting state to be IN_MATCHES after seeing
I token, so we don't print two successive ^ tokens.
* stage3.c: Added a pass to remove adjacent insertions and deletions and fix
single gaps again.
2012-01-10 twu