ChangeLog

+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:

VERSION

-2018-09-27
\ No newline at end of file
+2019-01-24
\ No newline at end of file

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for gmap 2018-09-27.
+# Generated by GNU Autoconf 2.69 for gmap 2019-01-24.
 #
 # Report bugs to <Thomas Wu <twu@gene.com>>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gmap'
 PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2018-09-27'
-PACKAGE_STRING='gmap 2018-09-27'
+PACKAGE_VERSION='2019-01-24'
+PACKAGE_STRING='gmap 2019-01-24'
 PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'
 PACKAGE_URL=''
@@ -1373,7 +1373,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gmap 2018-09-27 to adapt to many kinds of systems.
+\`configure' configures gmap 2019-01-24 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1444,7 +1444,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gmap 2018-09-27:";;
+     short | recursive ) echo "Configuration of gmap 2019-01-24:";;
    esac
   cat <<\_ACEOF
@@ -1585,7 +1585,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gmap configure 2018-09-27
+gmap configure 2019-01-24
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2191,7 +2191,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by gmap $as_me 2018-09-27, which was
+It was created by gmap $as_me 2019-01-24, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2541,8 +2541,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking package version" >&5
 $as_echo_n "checking package version... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2018-09-27" >&5
-$as_echo "2018-09-27" >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2019-01-24" >&5
+$as_echo "2019-01-24" >&6; }
 ### Read defaults
@@ -4409,7 +4409,7 @@ fi
 # Define the identity of the package.
  PACKAGE='gmap'
- VERSION='2018-09-27'
+ VERSION='2019-01-24'
 cat >>confdefs.h <<_ACEOF
@@ -19937,7 +19937,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gmap $as_me 2018-09-27, which was
+This file was extended by gmap $as_me 2019-01-24, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -20003,7 +20003,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-gmap config.status 2018-09-27
+gmap config.status 2019-01-24
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

debian/changelog

+gmap (2019-01-24-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+
+ -- Andreas Tille <tille@debian.org>  Thu, 31 Jan 2019 14:07:07 +0100
+
 gmap (2018-09-27-2) experimental; urgency=medium
 
   * Add patch supposedly fixing builds on MIPS and ARM architectures

debian/compat

-11
+12

debian/control

@@ -6,12 +6,12 @@ Uploaders: Shaun Jackman <sjackman@debian.org>,
 Section: non-free/science
 XS-Autobuild: yes
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-exec,
                help2man,
                libbz2-dev,
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/gmap
 Vcs-Git: https://salsa.debian.org/med-team/gmap.git
 Homepage: http://research-pub.gene.com/gmap

debian/patches/bigendian.patch

 Subject: Update bigendian.[c,h] files in attempt to fix builds on arm and mips
 Author: Upstream
 Forwarded: not-needed
---- gmap.orig/src/bigendian.c
-+++ gmap/src/bigendian.c
-@@ -18,6 +18,45 @@
-   return;
+--- a/src/bigendian.c
++++ b/src/bigendian.c
+@@ -19,6 +19,45 @@ Bigendian_write_char (unsigned char valu
  }
  
+ 
 +
 +/************************************************************************
 + *   Unsigned short
@@ -47,13 +47,13 @@ Forwarded: not-needed
 +
 +
  /************************************************************************
-  *   Int
+  *   Unsigned short
   ************************************************************************/
---- gmap.orig/src/bigendian.h
-+++ gmap/src/bigendian.h
-@@ -98,6 +98,9 @@
- #define FWRITE_UINT8S(a,n,fp) Bigendian_fwrite_uint8s(a,n,fp)
- #endif
+--- a/src/bigendian.h
++++ b/src/bigendian.h
+@@ -101,6 +101,9 @@ Bigendian_fwrite_double (double value, F
+ #define FWRITE_USHORT(x,fp) Bigendian_fwrite_ushort(x,fp)
+ #define FWRITE_USHORTS(a,n,fp) Bigendian_fwrite_ushorts(a,n,fp)
  
 +#define FWRITE_USHORT(x,fp) Bigendian_fwrite_ushort(x,fp)
 +#define FWRITE_USHORTS(a,n,fp) Bigendian_fwrite_ushorts(a,n,fp)

debian/rules

@@ -37,7 +37,9 @@ override_dh_install:
 	done
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test --no-parallel
+endif
 
 override_dh_installexamples:
 	mkdir $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples

src/access.c

-static char rcsid[] = "$Id: access.c 213998 2018-03-03 04:59:34Z twu $";
+static char rcsid[] = "$Id: access.c 218147 2019-01-16 21:28:41Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -690,13 +690,16 @@ shmem_attach (int *shmid, key_t *key, char *filename, size_t filesize, size_t el
 			 0666)) != -1) {
       /* Created new shared memory */
       if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
-	fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
+	fprintf(stderr,"Error with shmat (1).  Error %d: %s\n",errno,strerror(errno));
+	exit(9);
+
       } else if (unload_shared_memory_p == true) {
 	semaphore_ids = Intlist_push(semaphore_ids,semid);
 	shmem_memory = List_push(shmem_memory,memory);
 	shmem_ids = Intlist_push(shmem_ids,*shmid);
 	copy_limited_from_file(memory,filename,filesize,eltsize);
 	donep = true;
+
       } else {
 	semaphore_ids = Intlist_push(semaphore_ids,semid);
 	shmem_memory = List_push(shmem_memory,memory);
@@ -709,7 +712,8 @@ shmem_attach (int *shmid, key_t *key, char *filename, size_t filesize, size_t el
     } else if ((*shmid = shmget(*key,0,0)) != -1) {
       /* Found existing shared memory */
       if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
-	fprintf(stderr,"Error with shmat.  Error %d: %s\n",errno,strerror(errno));
+	fprintf(stderr,"Error with shmat (2).  Error %d: %s\n",errno,strerror(errno));
+	exit(9);
 	
       } else if ((nattached = shmem_nattached(*shmid)) > 1) {
 	/* Existing memory is indeed valid: attached (by a process other than this one) */
@@ -1009,9 +1013,9 @@ Access_mmap (int *fd, size_t *len, char *filename, bool randomp) {
 		  ,*fd,0);
 
     if (memory == MAP_FAILED) {
-      fprintf(stderr,"Error in access.c (1): Got mmap failure on len %jd from length %jd.  Error %d: %s\n",
-	      length,length,errno,strerror(errno));
-      debug(printf("Got MAP_FAILED on len %jd from length %jd\n",length,length));
+      fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd.  Error %d: %s\n",
+	      filename,length,errno,strerror(errno));
+      debug(printf("Got MAP_FAILED on file %s with length %jd\n",filename,length));
       memory = (void *) NULL;
 
     } else if (randomp == true) {
@@ -1149,9 +1153,9 @@ Access_mmap_rw (int *fd, size_t *len, char *filename, bool randomp) {
 		  ,*fd,0);
 
     if (memory == MAP_FAILED) {
-      fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd.  Error %d: %s\n",
-	      *len,length,errno,strerror(errno));
-      debug(printf("Got MAP_FAILED on len %zu from length %jd\n",*len,length));
+      fprintf(stderr,"Error in access.c (3): Got mmap failure on file %s with len %jd from length %jd.  Error %d: %s\n",
+	      filename,*len,length,errno,strerror(errno));
+      debug(printf("Got MAP_FAILED on file %s with len %zu from length %jd\n",filename,*len,length));
       memory = (void *) NULL;
 
     } else if (randomp == true) {
@@ -1303,9 +1307,9 @@ Access_mmap_and_preload (int *fd, size_t *len, int *npages, double *seconds, cha
 		  ,*fd,0);
 
     if (memory == MAP_FAILED) {
-      fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd.  Error %d: %s\n",
-	      *len,length,errno,strerror(errno));
-      debug(printf("Got MAP_FAILED on len %jd from length %zu\n",*len,length));
+      fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd.  Error %d: %s\n",
+	      filename,*len,length,errno,strerror(errno));
+      debug(printf("Got MAP_FAILED on file %s with len %jd from length %zu\n",filename,*len,length));
       memory = (void *) NULL;
       Stopwatch_stop(stopwatch);
       Stopwatch_free(&stopwatch);

src/atoiindex.c

-static char rcsid[] = "$Id: atoiindex.c 215536 2018-05-30 21:51:32Z twu $";
+static char rcsid[] = "$Id: atoiindex.c 218151 2019-01-17 05:36:54Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -59,6 +59,7 @@ static char rcsid[] = "$Id: atoiindex.c 215536 2018-05-30 21:51:32Z twu $";
 #include "genomicpos.h"
 #include "iit-read-univ.h"
 #include "indexdb.h"
+#include "indexdbdef.h"
 #include "indexdb-write.h"
 #include "genome.h"
 #include "genome128_hr.h"
@@ -730,10 +731,11 @@ sort_positions (char *ptrsfile, char *compfile, FILE *positions_high_fp, FILE *p
 }
 
 
+#if 0
 /*                                       G  C  G  T */
 static unsigned char ag_conversion[4] = {2, 1, 2, 3};
 static char AG_CHARTABLE[4] = {'G','C','G','T'};
-
+#endif
 
 static void
 compute_ag_local (char *new_region_filename,char *new_pointers_filename,
@@ -996,7 +998,7 @@ compute_ag (char *new_pointers_filename, char *new_offsets_filename,
   newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
   newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
 #endif
-  countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
+  countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,index1part);
 
   for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
     Bitpack64_block_offsets(oldoffsets,oligoi,indexdb->offsetsmeta,indexdb->offsetsstrm);
@@ -1093,9 +1095,11 @@ compute_ag (char *new_pointers_filename, char *new_offsets_filename,
 }
 
 
+#if 0
 /*                                       A  C  G  C */
 static unsigned char tc_conversion[4] = {0, 1, 2, 1};
 static char TC_CHARTABLE[4] = {'A','C','G','C'};
+#endif
 
 static void
 compute_tc_local (char *new_region_filename, char *new_pointers_filename,
@@ -1360,7 +1364,7 @@ compute_tc (char *new_pointers_filename, char *new_offsets_filename,
   newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
   newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
 #endif
-  countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
+  countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,index1part);
 
   for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
     Bitpack64_block_offsets(oldoffsets,oligoi,indexdb->offsetsmeta,indexdb->offsetsstrm);
@@ -1558,7 +1562,7 @@ main (int argc, char *argv[]) {
   if ((localdb = Localdb_new_genome(&local1part,&local1interval,
 				    sourcedir,fileroot,IDX_FILESUFFIX,/*snps_root*/NULL,
 				    required_local1part,required_local1interval,
-				    /*expand_offsets_p*/false,/*locoffsetsstrm_access*/USE_ALLOCATE,
+				    /*locoffsetsstrm_access*/USE_ALLOCATE,
 				    /*locpositions_access*/USE_ALLOCATE,/*sharedp*/false,
 				    /*multiple_sequences_p*/false,/*unload_shared_memory_p*/false)) != NULL) {
     local_mask = ~(~0U << 2*local1part);
@@ -1627,7 +1631,7 @@ main (int argc, char *argv[]) {
 				    required_index1part,required_index1interval,
 				    /*expand_offsets_p*/false,/*offsetsstrm_access*/USE_ALLOCATE,
 				    /*positions_access*/USE_ALLOCATE,/*sharedp*/false,
-				    /*multiple_sequences_p*/false,/*unload_shared_memory_p*/false)) != NULL) {
+				    /*multiple_sequences_p*/false,/*preload_shared_memory_p*/false,/*unload_shared_memory_p*/false)) != NULL) {
 #ifdef HAVE_64_BIT
     index_mask = ~(~0ULL << 2*index1part);
 #else

src/bigendian.c

-static char rcsid[] = "$Id: bigendian.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: bigendian.c 216772 2018-10-03 21:26:53Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -18,6 +18,45 @@ Bigendian_write_char (unsigned char value, int fd) {
   return;
 }
 
+
+/************************************************************************
+ *   Unsigned short
+ ************************************************************************/
+
+size_t
+Bigendian_fwrite_ushort (unsigned short value, FILE *fp) {
+  unsigned char buf[2];
+
+  buf[1] = value & 0xff;
+  buf[0] = (value >>= 8) & 0xff;
+  if (fwrite(buf,sizeof(unsigned short),2,fp) == 0) {
+    /* Should set error indicator for stream and set errno */
+    return 0;
+  } else {
+    return 1;
+  }
+}
+
+size_t
+Bigendian_fwrite_ushorts (unsigned short *array, int n, FILE *fp) {
+  unsigned char buf[4];
+  unsigned short value;
+  int i;
+  
+  for (i = 0; i < n; i++) {
+    value = array[i];
+    buf[1] = value & 0xff;
+    buf[0] = (value >>= 8) & 0xff;
+    if (fwrite(buf,sizeof(unsigned short),2,fp) == 0) {
+      /* Should set error indicator for stream and set errno */
+      return 0;
+    }
+  }
+  return n;
+}
+
+
+
 /************************************************************************
  *   Int
  ************************************************************************/

src/bigendian.h

-/* $Id: bigendian.h 168395 2015-06-26 17:13:13Z twu $ */
+/* $Id: bigendian.h 216772 2018-10-03 21:26:53Z twu $ */
 #ifndef BIGENDIAN_INCLUDED
 #define BIGENDIAN_INCLUDED
 #ifdef HAVE_CONFIG_H
@@ -98,6 +98,9 @@ Bigendian_fwrite_double (double value, FILE *fp);
 #define FWRITE_UINT8S(a,n,fp) Bigendian_fwrite_uint8s(a,n,fp)
 #endif
 
+#define FWRITE_USHORT(x,fp) Bigendian_fwrite_ushort(x,fp)
+#define FWRITE_USHORTS(a,n,fp) Bigendian_fwrite_ushorts(a,n,fp)
+
 #define FREAD_CHARS(a,n,fp) fread(a,sizeof(char),n,fp)
 #define FWRITE_CHARS(a,n,fp) fwrite(a,sizeof(char),n,fp)
 

src/bitpack64-write.c

-static char rcsid[] = "$Id: bitpack64-write.c 212659 2018-01-20 00:58:14Z twu $";
+static char rcsid[] = "$Id: bitpack64-write.c 216944 2018-10-10 07:14:00Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -5358,7 +5358,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
 
   /* Write pages */
   if (pagei > 0) {
-    pages[pagei++] = -1U; /* Final value */
+    pages[pagei++] = (UINT4) -1; /* Final value */
     if ((pages_fp = FOPEN_WRITE_BINARY(pagesfile)) == NULL) {
       fprintf(stderr,"Can't write to file %s\n",pagesfile);
       exit(9);
@@ -5521,7 +5521,7 @@ Bitpack64_write_differential_huge_bitpacks (char *pagesfile, char *ptrsfile, cha
 
   /* Write pages */
   if (pagei > 0) {
-    pages[pagei++] = -1U; /* Final value */
+    pages[pagei++] = (UINT4) -1; /* Final value */
     if ((pages_fp = FOPEN_WRITE_BINARY(pagesfile)) == NULL) {
       fprintf(stderr,"Can't write to file %s\n",pagesfile);
       exit(9);
@@ -5717,7 +5717,7 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
 
   /* Write pages */
   if (pagei > 0) {
-    pages[pagei++] = -1U; /* Final value */
+    pages[pagei++] = (UINT4) -1; /* Final value */
     if ((pages_fp = FOPEN_WRITE_BINARY(pagesfile)) == NULL) {
       fprintf(stderr,"Can't write to file %s\n",pagesfile);
       exit(9);

src/block.c

-static char rcsid[] = "$Id: block.c 214447 2018-03-26 03:17:38Z twu $";
+static char rcsid[] = "$Id: block.c 218152 2019-01-17 05:37:56Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -423,8 +423,7 @@ Block_process_oligo (Univcoord_T **fwdpositions, int *nfwdhits,
 int
 Block_process_oligo_5 (Univcoord_T **fwdpositions, int *nfwdhits,
 		       Univcoord_T **revpositions, int *nrevhits,
-		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
-		       int indexdb_sizelimit) {
+		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev) {
 #if 0
   printf("block_process: Querypos %d, oligos are %06X and %06X\n",this->last_querypos,this->forward,this->revcomp >> this->leftreadshift);
 #endif
@@ -440,8 +439,7 @@ Block_process_oligo_5 (Univcoord_T **fwdpositions, int *nfwdhits,
 int
 Block_process_oligo_3 (Univcoord_T **fwdpositions, int *nfwdhits,
 		       Univcoord_T **revpositions, int *nrevhits,
-		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
-		       int indexdb_sizelimit) {
+		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev) {
 #if 0
   printf("block_process Querypos %d, oligos are %06X and %06X\n",this->last_querypos,this->forward >> this->leftreadshift,this->revcomp);
 #endif

src/block.h

-/* $Id: block.h 214025 2018-03-05 07:06:43Z twu $ */
+/* $Id: block.h 218152 2019-01-17 05:37:56Z twu $ */
 #ifndef BLOCK_INCLUDED
 #define BLOCK_INCLUDED
 
@@ -56,13 +56,11 @@ Block_skip_3 (T this, int genestrand, int nskip);
 extern int
 Block_process_oligo_5 (Univcoord_T **fwdpositions, int *nfwdhits, 
 		       Univcoord_T **revpositions, int *nrevhits,
-		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
-		       int indexdb_sizelimit);
+		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev);
 extern int
 Block_process_oligo_3 (Univcoord_T **fwdpositions, int *nfwdhits, 
 		       Univcoord_T **revpositions, int *nrevhits,
-		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
-		       int indexdb_sizelimit);
+		       T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev);
 
 #undef T
 #endif

src/boyer-moore.h

-/* $Id: boyer-moore.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: boyer-moore.h 218147 2019-01-16 21:28:41Z twu $ */
 #ifndef BOYER_MOORE_INCLUDED
 #define BOYER_MOORE_INCLUDED
 
 #include "intlist.h"
 #include "genomicpos.h"
+#include "univcoord.h"
+
 
 extern Intlist_T
 BoyerMoore (char *query, int querylen, char *text, int textlen);

src/cellpool.c

-static char rcsid[] = "$Id: cellpool.c 212659 2018-01-20 00:58:14Z twu $";
+static char rcsid[] = "$Id: cellpool.c 218147 2019-01-16 21:28:41Z twu $";
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -48,28 +48,6 @@ struct T {
   List_T listcellchunks;
 };
 
-void
-Cellpool_free (T *old) {
-  List_T p;
-  struct Cell_T *objectptr;
-  struct List_T *listcellptr;
-
-  if (*old) {
-    for (p = (*old)->objectchunks; p != NULL; p = List_next(p)) {
-      objectptr = (struct Cell_T *) List_head(p);
-      FREE(objectptr);
-    }
-    List_free(&(*old)->objectchunks);
-    for (p = (*old)->listcellchunks; p != NULL; p = List_next(p)) {
-      listcellptr = (struct List_T *) List_head(p);
-      FREE(listcellptr);
-    }
-    List_free(&(*old)->listcellchunks);
-    FREE(*old);
-  }
-  return;
-}
-
 void
 Cellpool_free_memory (T this) {
   List_T p;
@@ -100,6 +78,13 @@ Cellpool_free_memory (T this) {
   return;
 }
 
+void
+Cellpool_free (T *old) {
+  Cellpool_free_memory(*old);
+  FREE_KEEP(*old);
+  return;
+}
+
 
 void
 Cellpool_report_memory (T this) {
@@ -139,7 +124,7 @@ add_new_listcellchunk (T this) {
 
 T
 Cellpool_new (void) {
-  T new = (T) MALLOC(sizeof(*new));
+  T new = (T) MALLOC_KEEP(sizeof(*new));
 
   new->nobjects = 0;
   new->objectctr = 0;

src/changepoint.h

+/* $Id: changepoint.h 218286 2019-01-23 16:46:55Z twu $ */
 #ifndef CHANGEPOINT_INCLUDED
 #define CHANGEPOINT_INCLUDED