New upstream version 2019-01-24

2019-01-23  twu

    * Makefile.gsnaptoo.am, VERSION, changepoint.h, compress.c, concordance.h,

      diag.c, extension-search.h, gbuffer.c, gbuffer.h, genome.c, genome.h,

      genome128_consec.c, genome128_hr.c, genome_hr.c, genome_sites.c, gmap.c,

      gsnap.c, kmer-search.c, kmer-search.h, knownsplicing.c, knownsplicing.h,

      oligoindex_localdb.h, outbuffer.h, output.c, pair.c, pair.h, path-solve.c,

      path-solve.h, samprint.c, segment-search.c, segment-search.h,

      simplepair.c, simplepair.h, splice.c, splice.h, splicetrie.c,

      splicetrie.h, splicetrie_build.h, src, stage1hr.c, stage1hr.h, stage3.c,

      stage3hr.c, stage3hr.h, substring.c, substring.h, trunk, types.h,

      univcoord.h, univdiagpool.c: Merged revisions 218195 through 218285 from

      branches/2019-01-17-split-gmap-gsnap to separate GMAP and GSNAP code

    * stage1hr.c: Added debugging statements

    * stage3hr.c: At a given locus, checking for nmatches_posttrim before

      checking for splice score

    * splice.c, splice.h, substring.c: Added limit on consecutive matches in

      scanning for spliceends

    * path-solve.c: Restored previous code that did not look at extendedp

    * splice.c: Added requirement for MIN_EXON_LENGTH in trimming ends

    * cigar.c, path-solve.c: Added debugging statements

    * gsnap.c: Added --sam_sparse_secondaries to omit SEQ and QUAL flags in

      secondary alignments

    * samprint.c, samprint.h: Using mate_plusp computed in Cigar_compute_main in

      compute_flag, to give correct results for translocations.  Added

      sam_sparse_secondaries_p to omit SEQ and QUAL flags in secondary

      alignments

2019-01-22  twu

    * path-solve.c: Restored usage of the sense condition to handle the

      non-splicing condition

    * filestring.c: Handling the case in Filestring_merge where source->string

      is NULL

    * path-solve.c: Checking if qstart or qend is extended from spliced

      endpoints of middle diagonal, and if not extended, using the original

      endpoints

    * junction.c: Changed name of macro for debugging

    * samprint.c: Handling the case where hard clipping removes all substrings

    * extension-search.c: Added debugging statement

    * cigar.c: Handling the case where hard clipping removes all substrings

2019-01-18  twu

    * extension-search.c: Fixed bugs in process_seed for processing the

      remainder of the queryfwd set or the queryrev set

    * extension-search.c: Rewrote algorithm extensively to combine seeds and

      sets from queryfwd and queryrev passes

    * segment-search.c: Using new interface to Path_solve_from_diagonals

    * path-solve.c, path-solve.h: Changed Path_solve_from_diagonals to take a

      univdiagonal, qstart, and qend, instead of a Univdiag_T object

    * kmer-search.c: Removed unused include file

2019-01-17  twu

    * setup.genomecomp.ok: Revised gold standard for extra bytes at end

    * segment-search.c: Fixed problem with allocation when total_npositions is

      zero in Segment_identify_lower and Segment_identify_higher

    * hitlistpool.c: Initial import

    * gsnap.c: Remoed oligoindices_major, oligoindices_minor, pairpool,

      diagpool, cellpool, and Dynprog_T objects as variables

    * gmap.c: Using new interfaces to stage1, stage2, and stage3 procedures

    * stage3.c, stage3.h: Removed unused parameters

    * translation.c: Removed npairs as a parameter for backward procedures

    * terminal.c, terminal.h: Removed mismatch_positions_alloc as a parameter

    * stage2.c: Removed code based on anchoredp, anchor_querypos, and

      anchor_position, which are now always false and 0

    * stage1hr.c, stage1hr.h: Using new interfaces to kmer-search,

      extension-search, terminal, and concordance procedures.  Removed

      oligoindices_minor, diagpool, and cellpool parameters to single_read and

      paired_read procedures

    * stage1.c, stage1.h: Using new interfaces to Block_process_oligo_5 and

      Block_process_oligo_3.  Removed sizelimit parameters to Stage1_compute

      procedures

    * splice.c, splice.h: Removed unused parameters to Splice_setup

    * smooth.c: Removed exon_denominator as a parameter to

      find_internal_bads_by_prob

    * segment-search.c: Removed unused variable

    * samprint.h: Removed preprocessor macros for GSNAP

    * samprint.c: Using new interfaces to Substring_compute_chrpos and

      Pair_print_sam

    * path-solve.h: Removed interface to Path_solve_via_gmap

    * path-solve.c: Using new interfaces to substring procedures

    * pair.c, pair.h: Removed unused parameters for Pair_print_sam

    * output.c: Using new interfaces to stage3 print procedures

    * iit-write-univ.c: Removed omegas as a parameter to node_select

    * iit-read.c, iit-read.h: Commented out obsolete procedure

    * genome128_consec.c: Added macros around some procedures.  Removed unused

      procedures

    * genome128_hr.c: Added macros around some procedures

    * intersect.c: Added LARGE_GENOMES macro to a procedure

    * indexdb.c: Added LARGE_GENOMES macro to a procedure

    * oligoindex_hr.c, oligoindex_hr.h: Removed unused parameters from

      Oligoindex_untally

    * kmer-search.c, kmer-search.h: Removed unused parameters

    * extension-search.c, extension-search.h: Removed unused parameters

    * epu16-bitpack64-read.c, epu16-bitpack64-readtwo.c: Commented out print

      procedures for debugging

    * epu16-bitpack64-incr.c: Turned off CHECK macro

    * dynprog_single.c, dynprog_single.h: Removed glengthL and glengthR as

      parameters to Dynprog_microexon_int

    * dynprog_genome.c, dynprog_genome.h: Removed unused parameters, including

      calculation of canonical_reward

    * distant-rna.c, distant-rna.h: Removed user_maxlevel as a parameter

    * datadir.c: Removed unused variables

    * concordance.c, concordance.h: Using new interface to Stage3pair_new. 

      Removed unused parameters

    * stage3hr.c, stage3hr.h: Removed oligoindices_minor, diagpool, and cellpool

      as parameters, used previously for resolving insides

    * compress-write.c: Using different format statements for Univcoord_T

      variables

    * cigar.c: Removed trimlength as a parameter to length_cigar_M.  Using new

      interface to Substring_compute_chrpos

    * substring.c, substring.h: Removed plusp as a parameter to

      embellish_genomic and hardclip_high as a parameter to

      Substring_compute_chrpos

    * reader.c, reader.h: Commented out unused procedures

    * block.c, block.h: Removed indexdb_sizelimit as a parameter to

      Block_process_oligo_5 and Block_process_oligo_3

    * atoiindex.c, cmetindex.c, snpindex.c: Using new interfaces to

      Indexdb_bitpack_counter and Localdb_new_genome

    * localdb.c, localdb.h: Removed expand_offsets_p as a parameter to

      Localdb_new_genome

    * indexdb-write.c, indexdb-write.h: Removed offsetsstrm and offsetspages as

      parameters to Indexdb_bitpack_counter and Indexdb_bitpack_counter_huge

2019-01-16  twu

    * Makefile.gsnaptoo.am, VERSION, access.c, atoiindex.c, boyer-moore.h,

      cellpool.c, chrom.h, cigar.c, cmetindex.c, compress-write.h,

      concordance.c, concordance.h, diag.h, diagpool.c, distant-rna.c,

      distant-rna.h, extension-search.c, extension-search.h, filestring.c,

      genome128_hr.c, genome_sites.h, genomicpos.c, gmap.c, gmapindex.c,

      gregion.c, gsnap.c, hitlistpool.h, indel.c, indexdb.c, indexdb.h,

      intersect-large.h, intersect.c, intersect.h, intlist.c, intlist.h,

      intlistdef.h, intlistpool.c, intlistpool.h, junction.c, junction.h,

      kmer-search.c, kmer-search.h, ladder.c, ladder.h, list.h, listdef.h,

      listpool.c, listpool.h, localdb.c, localdb.h, localdbdef.h, matchpool.c,

      maxent_hr.h, mem.h, merge-diagonals-heap.h, merge-diagonals-simd-uint4.c,

      merge-diagonals-simd-uint4.h, merge-diagonals-simd-uint8.h, merge-uint4.c,

      method.c, oligoindex_hr.c, oligoindex_hr.h, outbuffer.c, outbuffer.h,

      output.c, output.h, pair.c, pair.h, pairpool.c, path-solve.c,

      path-solve.h, result.h, resulthr.h, samprint.c, samprint.h,

      segment-search.c, segment-search.h, shortread.c, shortread.h, splice.c,

      splice.h, splicestringpool.c, splicetrie.c, splicetrie_build.h, src,

      stage1hr.c, stage1hr.h, stage3.c, stage3.h, stage3hr.c, stage3hr.h,

      stage3hrdef.h, substring.c, substring.h, terminal.c, terminal.h, trunk,

      types.h, uint8listpool.c, uint8listpool.h, uint8table_rh.c,

      uint8table_rh.h, uintlist.c, uintlist.h, uintlistpool.c, uintlistpool.h,

      uinttable.c, uinttable_rh.c, uinttable_rh.h, uniqscan.c, univcoord.h,

      univdiag.c, univdiag.h, univdiagdef.h, univdiagpool.c, univdiagpool.h,

      univinterval.h: Merged revisions 216893 to 218146 from

      branches/2018-10-08-path-solve to improve path-solve procedure

2018-10-18  twu

    * genome-write.c: Adding 2 words to the end of genomecomp, needed for

      accessing nextlow (ptr+4) in the fwd_partial and rev_partial procedures in

      oligoindex_hr.c

2018-10-10  twu

    * genome.c: Replaced occurrences of 1U with 1

    * bitpack64-serial-write.c, bitpack64-write.c, genome-write.c, genome.c,

      genome128.c, gmapindex.c, indexdb-write.c, indexdb.c, indexdb_hr.c,

      kmer-search.c, outbuffer.c, pair.c, parserange.c, stage3.c, stage3hr.c,

      substring.c: Replaced occurrences of 1U with 1

    * sedgesort.c: Fixed bug in Sedgesort_uint8 where we assigned -1U instead of

      (UINT8) -1 as the sentinel value

    * path-solve.c: Removing endpoints from the left and right to see if a

      continuing alignment works

    * Makefile.gsnaptoo.am, concordance.c, concordance.h, distant-rna.c,

      distant-rna.h, extension-search.c, extension-search.h, gsnap.c,

      intlistpool.c, junction.c, junction.h, kmer-search.c, kmer-search.h,

      list.h, listpool.c, listpool.h, pair.c, pair.h, path-solve.c,

      path-solve.h, segment-search.c, segment-search.h, src, stage1hr.c,

      stage1hr.h, stage3hr.c, stage3hr.h, terminal.c, terminal.h, trunk: Merged

      revision 216940 from branches/2018-10-10-reduce-list-push to add

      Listpool_T object for lists of substrings and junctions

2018-10-09  twu

    * Makefile.gsnaptoo.am, VERSION, intersect-large.c, intersect-large.h,

      intersect.c, intersect.h, path-solve.c, record.h, segment-search.c,

      segment-search.h, src, stage1hr.c, stage1hr.h, trunk: Merged revisions

      216922 through 216936 from branches/2018-10-09-merge-records to replace

      Merge_records procedures in segment search with Merge_diagonals

    * localdb.c: Allocating extra space for array, needed for Sedgesort

    * concordance.c: Removed unused code for filtering paired-end hits

    * concordance.c: Restored computation of abort_pairing_p

    * Makefile.gsnaptoo.am, VERSION, distant-rna.c, distant-rna.h,

      extension-search.c, filter-diagonals.c, filter-diagonals.h, gsnap.c,

      kmer-search.c, kmer-search.h, localdb.c, localdb.h,

      merge-diagonals-heap.c, merge-diagonals-heap.h,

      merge-diagonals-simd-uint4.c, merge-diagonals-simd-uint4.h,

      merge-diagonals-simd-uint8.c, merge-diagonals-simd-uint8.h,

      merge-records-heap.c, merge-records-heap.h, merge-records-simd.c,

      merge-records-simd.h, merge-uint4.c, path-solve.c, path-solve.h,

      segment-search.c, segment-search.h, splice.c, splice.h, src, stage1hr.c,

      stage1hr.h, stage3hr.c, stage3hr.h, substring.c, substring.h, terminal.c,

      terminal.h, trunk: Merged revisions 216889 to 216917 from

      branches/2018-10-07-filter-diagonals to introduce a filtering step before

      segment search, and to pre-allocate memory for Merge_records,

      Merge_diagonals, Splice_resolve, and Substring_new procedures

    * kmer-search.c, src: Fixed double-assignment of variable

2018-10-08  twu

    * method.c, method.h, segment-search.c, segment-search.h, stage1hr.c:

      Distinguishing between segment search for single-end reads and segment

      search for anchored paired-end reads

2018-10-07  twu

    * Makefile.gsnaptoo.am, VERSION, concordance.c, concordance.h,

      config.site.rescomp.prd, extension-search.c, extension-search.h, gsnap.c,

      intersect-large.c, intersect-large.h, intersect.c, intersect.h,

      intlistpool.c, intlistpool.h, intpool.c, intpool.h, kmer-search.c,

      kmer-search.h, ladder.c, ladder.h, localdb.c, mem.h,

      merge-diagonals-heap.c, merge-diagonals-heap.h,

      merge-diagonals-simd-uint4.c, merge-diagonals-simd-uint4.h,

      merge-diagonals-simd-uint8.c, merge-diagonals-simd-uint8.h,

      merge-heap-diagonals.c, merge-heap-diagonals.h, merge-heap-records.c,

      merge-heap-records.h, merge-records-heap.c, merge-records-heap.h,

      merge-records-simd.c, merge-records-simd.h, merge-simd-diagonals.c,

      merge-simd-diagonals.h, merge-simd-records.c, merge-simd-records.h,

      merge-uint4.h, merge-uint8.c, merge-uint8.h, method.c, method.h,

      path-solve.c, path-solve.h, sedgesort.c, sedgesort.h, segment-search.c,

      segment-search.h, src, stage1hr.c, stage1hr.h, stage3hr.c, trunk: Merged

      revisions 216741 to 216887 from branches/2018-10-01-gsnapl-speed to

      increased speed of GSNAP and GSNAPL, especially for paired-end reads

    * index.html: Updated for current version

2018-10-03  twu

    * concordance.c, concordance.h, stage1hr.c: Using new interfaces to

      Stage3pair_new and Concordance_pair_up procedures

    * stage3hr.c, stage3hr.h: No longer filtering substrings based on

      endtrim_allowed on one side. Performing resolve_insides at end of

      Stage3pair_new

    * segment-search.c: Fixed debugging statements

    * path-solve.c: No longer calling a check creation of a substring of the

      middle diagonal

    * kmer-search.c: Hiding a debugging procedure

    * acinclude.m4, configure.ac, genome128_consec.c, genome128_hr.c,

      simd-intrinsics.m4: Added compiler checks for the SIMD intrinsics

      _mm_extract_epi64 and _mm_popcnt_u64, and using them

    * extension-search.c: Removed unused debugging procedure

    * epu16-bitpack64-write.c: Modified comments

    * bigendian.c, bigendian.h: Implemented FWRITE_USHORT and FWRITE_USHORTS for

      bigendian machines

    * substring.c: Fixed uninitialized fields querystart_pretrim and

      queryend_pretrim in Substring_T object

2018-07-06  twu

    * VERSION, config.site.rescomp.tst, index.html, path-solve.c, src, trunk:

2018-09-27

 No newline at end of file

2019-01-24

 No newline at end of file

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