@@ -116,3 +116,4 @@ src/gstruct/src/stamp-h1

 inst/user

 inst/usr

 /src/samtools/libbam.a

+/src/gstruct/src/libgstruct_1.0_la-expr.lo

@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.27.1

+Version: 1.27.2

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)

 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),

@@ -17,9 +17,11 @@ setClass("BamTallyParam",

                         ignore_duplicates = "logical",

                         min_depth = "integer",

                         variant_strand = "integer",

+                        variant_pct = "numeric",

                         ignore_query_Ns = "logical",

                         indels = "logical",

-                        include_soft_clips = "integer",

+                        min_softclip = "integer",

+                        max_softclip = "integer",

                         exon_iit = "character_OR_NULL",

                         xs = "logical",

                         read_pos = "logical",

@@ -103,9 +105,9 @@ BamTallyParam <- function(genome, which = GRanges(),

                           desired_read_group = NULL, minimum_mapq = 0L,

                           concordant_only = FALSE, unique_only = FALSE,

                           primary_only = FALSE, ignore_duplicates = FALSE,

-                          min_depth = 0L, variant_strand = 0L,

+                          min_depth = 0L, variant_strand = 0L, variant_pct = 0,

                           ignore_query_Ns = FALSE,

-                          indels = FALSE, include_soft_clips = 0L,

+                          indels = FALSE, min_softclip = 0L, max_softclip = 0L,

                           exon_iit = NULL, IIT_BPPARAM = NULL,

                           xs = FALSE, read_pos = FALSE,

                           min_base_quality = 0L, noncovered = FALSE,

@@ -127,12 +129,18 @@ BamTallyParam <- function(genome, which = GRanges(),

     stop("min_depth must be a single, non-negative, non-NA number")

   if (!variant_strand %in% c(0, 1, 2))

     stop("variant_strand must be one of 0, 1, or 2")

+  if (variant_pct < 0)

+    stop("variant_pct must be non-negative")

   if (!isTRUEorFALSE(ignore_query_Ns))

     stop("ignore_query_Ns must be TRUE or FALSE")

   if (!isTRUEorFALSE(indels))

     stop("indels must be TRUE or FALSE")

-  if (include_soft_clips < 0)

-    stop("include_soft_clips must be non-negative")

+  if (max_softclip < 0L)

+    stop("max_softclip must be non-negative")

+  if (min_softclip < 0L)

+    stop("min_softclip must be non-negative")

+  if (max_softclip < min_softclip)

+    stop("max_softclip must be at least equal to min_softclip")

   if (!isTRUEorFALSE(xs))

     stop("xs must be TRUE or FALSE")

   if (!isTRUEorFALSE(read_pos))

@@ -149,7 +157,7 @@ BamTallyParam <- function(genome, which = GRanges(),

   params$which <- normArgWhich(which, params$genome)

   params$exon_iit = normArgCdsIIT(params$exon_iit, BPPARAM = IIT_BPPARAM)

   integer_params <- c("minimum_mapq", "min_depth", "variant_strand",

-                      "include_soft_clips")

+                      "min_softclip", "max_softclip")

   params[integer_params] <- lapply(params[integer_params], as.integer)

   params = params[names(params) != "IIT_BPPARAM"]

   do.call(new, c("BamTallyParam", params))  

@@ -205,6 +205,13 @@ normArgSingleInteger <- function(x) {

     stop("'", name, "' should be a single, non-NA integer")

   x

 }

+normArgSingleNumber <- function(x) {

+    name <- deparse(substitute(x))

+    x <- as.numeric(x)

+    if (!isSingleNumber(x))

+        stop("'", name, "' should be a single, non-NA number")

+    x

+}

 normArgTRUEorFALSE <- function(x) {

   name <- deparse(substitute(x))

   if (!isTRUEorFALSE(x))

@@ -227,11 +234,11 @@ normArgSingleCharacterOrNULL <- function(x) {

                          maximum_nhits = 1000000L,

                          concordant_only = FALSE, unique_only = FALSE,

                          primary_only = FALSE, ignore_duplicates = FALSE,

-                         min_depth = 0L, variant_strand = 0L,

+                         min_depth = 0L, variant_strand = 0L, variant_pct = 0,

                          ignore_query_Ns = FALSE,

                          indels = FALSE,

                          blocksize = 1000L, verbosep = FALSE,

-                         include_soft_clips = 0L,

+                         min_softclip = 0L, max_softclip = 0L,

                          exon_iit = NULL, xs = FALSE, read_pos = FALSE,

                          min_base_quality = 0L, noncovered = FALSE, nm = FALSE)

 {

@@ -258,11 +265,13 @@ normArgSingleCharacterOrNULL <- function(x) {

         normArgTRUEorFALSE(ignore_duplicates),

         normArgSingleInteger(min_depth),

         normArgSingleInteger(variant_strand),

+        normArgSingleNumber(variant_pct),

         normArgTRUEorFALSE(ignore_query_Ns),

         normArgTRUEorFALSE(indels),

         normArgSingleInteger(blocksize),

         normArgTRUEorFALSE(verbosep),

-        normArgSingleInteger(include_soft_clips),

+        normArgSingleInteger(min_softclip),

+        normArgSingleInteger(max_softclip),

         normArgSingleCharacterOrNULL(exon_iit),

         normArgTRUEorFALSE(xs),

         normArgTRUEorFALSE(read_pos),

@@ -8,9 +8,9 @@ test_BamTallyParam <- function() {

                minimum_mapq = 0L,

                concordant_only = FALSE, unique_only = FALSE,

                primary_only = FALSE, ignore_duplicates = FALSE,

-               min_depth = 0L, variant_strand = 0L,

+               min_depth = 0L, variant_strand = 0L, variant_pct = 0,

                ignore_query_Ns = FALSE,

-               indels = FALSE, include_soft_clips = 0L,

+               indels = FALSE, min_softclip = 0L, max_softclip = 0L,

                xs = FALSE, read_pos = FALSE, min_base_quality = 0L,

                noncovered = FALSE, nm = FALSE)

   which <- TP53Which()

@@ -19,9 +19,9 @@

                 minimum_mapq = 0L,

                 concordant_only = FALSE, unique_only = FALSE,

                 primary_only = FALSE, ignore_duplicates = FALSE,

-                min_depth = 0L, variant_strand = 0L,

+                min_depth = 0L, variant_strand = 0L, variant_pct = 0,

                 ignore_query_Ns = FALSE,

-                indels = FALSE, include_soft_clips = 0L,

+                indels = FALSE, min_softclip = 0L, max_softclip = 0L,

                 exon_iit = NULL, IIT_BPPARAM = NULL,

                 xs = FALSE, read_pos = FALSE,

                 min_base_quality = 0L, noncovered = FALSE, nm = FALSE)

@@ -52,6 +52,8 @@

     only positions where a variant was seen on at least one strand, and

     2 requires the variant be seen on both strands. Setting this to 1

     is a good way to save resources.}

+  \item{variant_pct}{The minimum alternate allele fraction

+    for a variant to be reported for a strand.} 

   \item{ignore_query_Ns}{Whether to ignore the N base pairs when

     counting. Can save a lot of resources when processing low quality data.}

   \item{indels}{Whether to return indel counts. The \code{ref} and

@@ -60,7 +62,8 @@

     always spans the sequence in \code{ref}; so e.g. a deletion extends

     one nt upstream of the actual deleted sequence.

   }

-  \item{include_soft_clips}{Maximum length of soft clips that are

+  \item{min_softclip, max_softclip}{

+    Minimum and maximum length of soft clips that are

     considered for counting. Soft-clipping is often useful (for GSNAP at

     least) during alignment, and it should be preserved in the

     output. However, soft clipping can preferentially occur in regions

@@ -7,7 +7,7 @@

 static const R_CallMethodDef callMethods[] = {

   /* bamtally.c */

-  CALLMETHOD_DEF(R_Bamtally_iit, 26),

+  CALLMETHOD_DEF(R_Bamtally_iit, 28),

   CALLMETHOD_DEF(R_tally_iit_parse, 6),

   /* bamreader.c */

@@ -19,11 +19,11 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP maximum_nhits_R,

                 SEXP need_concordant_p_R, SEXP need_unique_p_R,

                 SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,

-                SEXP min_depth_R, SEXP variant_strands_R,

+                SEXP min_depth_R, SEXP variant_strands_R, SEXP variant_pct_R,

                 SEXP ignore_query_Ns_p_R,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R, SEXP max_softclip_R,

+                SEXP verbosep_R, SEXP min_softclip_R, SEXP max_softclip_R,

                 SEXP exon_iit_file_R,

                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,

                 SEXP minimum_quality_score_R, SEXP noncovered_R,

@@ -34,6 +34,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

     genome_dir_R == R_NilValue ? NULL : CHAR(asChar(genome_dir_R));

   const char *db = CHAR(asChar(db_R));

   int alloclength = asInteger(alloclength_R);

+  int pastlength = alloclength;

   const char *desired_read_group =

     desired_read_group_R == R_NilValue ? NULL :

     CHAR(asChar(desired_read_group_R));

@@ -46,10 +47,12 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

   bool ignore_duplicates_p = asLogical(ignore_duplicates_p_R);

   int min_depth = asInteger(min_depth_R);

   int variant_strands = asInteger(variant_strands_R);

+  double variant_pct = asReal(variant_pct_R);

   bool ignore_query_Ns_p = asLogical(ignore_query_Ns_p_R);

   bool print_indels_p = asLogical(print_indels_p_R);

   int blocksize = asInteger(blocksize_R);

   int verbosep = asLogical(verbosep_R);

+  int min_softclip = asInteger(min_softclip_R);

   int max_softclip = asInteger(max_softclip_R);

   bool print_xs_scores_p = asLogical(print_xs_scores_p_R);

   bool print_cycles_p = asLogical(print_cycles_p_R);

@@ -79,7 +82,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  genome,

                                  chromosome_iit,

                                  map_iit,

-                                 alloclength,

+                                 alloclength, pastlength,

                                  (char *)desired_read_group,

                                  minimum_mapq, good_unique_mapq,

                                  minimum_quality_score,

@@ -87,10 +90,11 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  need_unique_p, need_primary_p,

                                  ignore_duplicates_p,

                                  min_depth, variant_strands,

-				 /* TODO: variant_pct */ 0,

+				 variant_pct,

 				 ignore_query_Ns_p,

                                  print_indels_p, blocksize, verbosep,

-                                 /*readlevel_p*/false, max_softclip,

+                                 /*readlevel_p*/false,

+				 min_softclip, max_softclip,

                                  print_cycles_p,

                                  print_nm_scores_p,

                                  print_xs_scores_p, noncovered_p);

@@ -16,14 +16,14 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP maximum_nhits_R,

                 SEXP need_concordant_p_R, SEXP need_unique_p_R,

                 SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,

-                SEXP min_depth_R, SEXP variant_strands_R,

-                SEXP ignore_query_Ns_p,

+                SEXP min_depth_R, SEXP variant_strands_R, SEXP variant_pct_R,

+                SEXP ignore_query_Ns_p_R,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R, SEXP max_softclip_R,

-                SEXP genome_iit_file_R,

+                SEXP verbosep_R, SEXP min_softclip_R, SEXP max_softclip_R,

+                SEXP exon_iit_file_R,

                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,

-                SEXP minimum_quality_score_R, SEXP nonconvered_R,

+                SEXP minimum_quality_score_R, SEXP noncovered_R,

                 SEXP print_nm_scores_p_R);

 SEXP

@@ -23,12 +23,12 @@ BAM_TALLY_FILES = fopen.h bool.h types.h bam.h bgzf.h \

  md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \

- translation.c translation.h bamtally.c bamtally.h \

+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \

  datadir.c datadir.h \

- getopt.c getopt1.c getopt.h bamtally_main.c

+ getline.c getline.h getopt.c getopt1.c getopt.h bamtally_main.c

 if HAVE_SAMTOOLS_LIB

 bam_tally_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_CFLAGS) $(POPCNT_FLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

@@ -48,10 +48,10 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.h \

  md5.c md5.h sequence.c sequence.h genome.c genome.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \

- translation.c translation.h bamtally.c bamtally.h \

+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \

  datadir.c datadir.h

 # Do not add SAMTOOLS LIBS here

@@ -167,12 +167,12 @@ am__dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES_DIST =  \

 	iit-read.c iit-read.h complement.h chrom.c chrom.h \

 	genomicpos.c genomicpos.h md5.c md5.h sequence.c sequence.h \

 	genome.c genome.h uinttable.c uinttable.h table.c table.h \

-	chrnum.c chrnum.h bamread.c bamread.h samread.c samread.h \

-	parserange.c parserange.h tableuint.c tableuint.h iit-write.c \

-	iit-write.h ucharlist.c ucharlist.h matchdef.h matchpool.c \

-	matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h \

-	tally.c tally.h translation.c translation.h bamtally.c \

-	bamtally.h datadir.c datadir.h

+	chrnum.c chrnum.h samflags.h bamread.c bamread.h samread.c \

+	samread.h parserange.c parserange.h tableuint.c tableuint.h \

+	iit-write.c iit-write.h ucharlist.c ucharlist.h matchdef.h \

+	matchpool.c matchpool.h mismatchdef.h mismatchpool.c \

+	mismatchpool.h tally.c tally.h translation.c translation.h \

+	expr.c expr.h bamtally.c bamtally.h datadir.c datadir.h

 am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-assert.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mem.lo \

@@ -203,6 +203,7 @@ am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-tally.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.lo \

+	libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo \

 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.lo

 @HAVE_SAMTOOLS_LIB_TRUE@dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_OBJECTS =  \

@@ -228,13 +229,14 @@ am__dist_bam_tally_SOURCES_DIST = fopen.h bool.h types.h bam.h bgzf.h \

 	access.h iitdef.h iit-read.c iit-read.h chrom.c chrom.h \

 	genomicpos.c genomicpos.h md5.c md5.h complement.h sequence.c \

 	sequence.h genome.c genome.h uinttable.c uinttable.h table.c \

-	table.h chrnum.c chrnum.h bamread.c bamread.h samread.c \

-	samread.h parserange.c parserange.h tableuint.c tableuint.h \

-	iit-write.c iit-write.h ucharlist.c ucharlist.h matchdef.h \

-	matchpool.c matchpool.h mismatchdef.h mismatchpool.c \

-	mismatchpool.h tally.c tally.h translation.c translation.h \

-	bamtally.c bamtally.h datadir.c datadir.h getopt.c getopt1.c \

-	getopt.h bamtally_main.c

+	table.h chrnum.c chrnum.h samflags.h bamread.c bamread.h \

+	samread.c samread.h parserange.c parserange.h tableuint.c \

+	tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

+	matchdef.h matchpool.c matchpool.h mismatchdef.h \

+	mismatchpool.c mismatchpool.h tally.c tally.h translation.c \

+	translation.h expr.c expr.h bamtally.c bamtally.h datadir.c \

+	datadir.h getline.c getline.h getopt.c getopt1.c getopt.h \

+	bamtally_main.c

 am__objects_2 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

 	bam_tally-mem.$(OBJEXT) bam_tally-intlist.$(OBJEXT) \

 	bam_tally-list.$(OBJEXT) bam_tally-littleendian.$(OBJEXT) \

@@ -250,7 +252,8 @@ am__objects_2 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \

 	bam_tally-iit-write.$(OBJEXT) bam_tally-ucharlist.$(OBJEXT) \

 	bam_tally-matchpool.$(OBJEXT) bam_tally-mismatchpool.$(OBJEXT) \

 	bam_tally-tally.$(OBJEXT) bam_tally-translation.$(OBJEXT) \

-	bam_tally-bamtally.$(OBJEXT) bam_tally-datadir.$(OBJEXT) \

+	bam_tally-expr.$(OBJEXT) bam_tally-bamtally.$(OBJEXT) \

+	bam_tally-datadir.$(OBJEXT) bam_tally-getline.$(OBJEXT) \

 	bam_tally-getopt.$(OBJEXT) bam_tally-getopt1.$(OBJEXT) \

 	bam_tally-bamtally_main.$(OBJEXT)

 @HAVE_SAMTOOLS_LIB_TRUE@dist_bam_tally_OBJECTS = $(am__objects_2)

@@ -492,12 +495,12 @@ BAM_TALLY_FILES = fopen.h bool.h types.h bam.h bgzf.h \

  md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \

- translation.c translation.h bamtally.c bamtally.h \

+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \

  datadir.c datadir.h \

- getopt.c getopt1.c getopt.h bamtally_main.c

+ getline.c getline.h getopt.c getopt1.c getopt.h bamtally_main.c

 @HAVE_SAMTOOLS_LIB_TRUE@bam_tally_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_CFLAGS) $(POPCNT_FLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"

 @HAVE_SAMTOOLS_LIB_TRUE@bam_tally_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)

@@ -513,10 +516,10 @@ LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.h \

  md5.c md5.h sequence.c sequence.h genome.c genome.h \

  uinttable.c uinttable.h table.c table.h \

  chrnum.c chrnum.h \

- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \

  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \

  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \

- translation.c translation.h bamtally.c bamtally.h \

+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \

  datadir.c datadir.h

@@ -707,8 +710,10 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrom.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-datadir.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-except.Po@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-expr.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genome.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genomicpos.Po@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getline.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt1.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-iit-read.Po@am__quote@

@@ -741,6 +746,7 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrom.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.Plo@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genome.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genomicpos.Plo@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-iit-read.Plo@am__quote@

@@ -996,6 +1002,13 @@ libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.lo: translation.c

 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.lo `test -f 'translation.c' || echo '$(srcdir)/'`translation.c

+libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo: expr.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -MT libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo `test -f 'expr.c' || echo '$(srcdir)/'`expr.c

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Tpo $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Plo

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo' libtool=yes @AMDEPBACKSLASH@

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo `test -f 'expr.c' || echo '$(srcdir)/'`expr.c

+

 libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo: bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS) $(CFLAGS) -MT libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo -MD -MP -MF $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Tpo -c -o libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo `test -f 'bamtally.c' || echo '$(srcdir)/'`bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Tpo $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Plo

@@ -1430,6 +1443,20 @@ bam_tally-translation.obj: translation.c

 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`

+bam_tally-expr.o: expr.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-expr.o -MD -MP -MF $(DEPDIR)/bam_tally-expr.Tpo -c -o bam_tally-expr.o `test -f 'expr.c' || echo '$(srcdir)/'`expr.c

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-expr.Tpo $(DEPDIR)/bam_tally-expr.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='bam_tally-expr.o' libtool=no @AMDEPBACKSLASH@

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-expr.o `test -f 'expr.c' || echo '$(srcdir)/'`expr.c

+

+bam_tally-expr.obj: expr.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-expr.obj -MD -MP -MF $(DEPDIR)/bam_tally-expr.Tpo -c -o bam_tally-expr.obj `if test -f 'expr.c'; then $(CYGPATH_W) 'expr.c'; else $(CYGPATH_W) '$(srcdir)/expr.c'; fi`

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-expr.Tpo $(DEPDIR)/bam_tally-expr.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='bam_tally-expr.obj' libtool=no @AMDEPBACKSLASH@

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-expr.obj `if test -f 'expr.c'; then $(CYGPATH_W) 'expr.c'; else $(CYGPATH_W) '$(srcdir)/expr.c'; fi`

+

 bam_tally-bamtally.o: bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-bamtally.o -MD -MP -MF $(DEPDIR)/bam_tally-bamtally.Tpo -c -o bam_tally-bamtally.o `test -f 'bamtally.c' || echo '$(srcdir)/'`bamtally.c

 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-bamtally.Tpo $(DEPDIR)/bam_tally-bamtally.Po

@@ -1458,6 +1485,20 @@ bam_tally-datadir.obj: datadir.c

 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`

+bam_tally-getline.o: getline.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-getline.o -MD -MP -MF $(DEPDIR)/bam_tally-getline.Tpo -c -o bam_tally-getline.o `test -f 'getline.c' || echo '$(srcdir)/'`getline.c

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-getline.Tpo $(DEPDIR)/bam_tally-getline.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='getline.c' object='bam_tally-getline.o' libtool=no @AMDEPBACKSLASH@

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-getline.o `test -f 'getline.c' || echo '$(srcdir)/'`getline.c

+

+bam_tally-getline.obj: getline.c

+@am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-getline.obj -MD -MP -MF $(DEPDIR)/bam_tally-getline.Tpo -c -o bam_tally-getline.obj `if test -f 'getline.c'; then $(CYGPATH_W) 'getline.c'; else $(CYGPATH_W) '$(srcdir)/getline.c'; fi`

+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-getline.Tpo $(DEPDIR)/bam_tally-getline.Po

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='getline.c' object='bam_tally-getline.obj' libtool=no @AMDEPBACKSLASH@

+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@

+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -c -o bam_tally-getline.obj `if test -f 'getline.c'; then $(CYGPATH_W) 'getline.c'; else $(CYGPATH_W) '$(srcdir)/getline.c'; fi`

+

 bam_tally-getopt.o: getopt.c

 @am__fastdepCC_TRUE@	$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(bam_tally_CFLAGS) $(CFLAGS) -MT bam_tally-getopt.o -MD -MP -MF $(DEPDIR)/bam_tally-getopt.Tpo -c -o bam_tally-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c

 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-getopt.Tpo $(DEPDIR)/bam_tally-getopt.Po

@@ -1317,7 +1317,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_

     fprintf(fp,"^");

     for (p = this->insertions_byshift; p != NULL; p = List_next(p)) {

       ins = (Insertion_T) List_head(p);

-      fprintf(fp,"%s %ld ref:%ld",

+      fprintf(fp,"%s %ld ref:%d",

 	      ins->segment,ins->count,

 	      insertion_refcount(&refcount_plus,ins,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     }

@@ -1329,7 +1329,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_

     fprintf(fp,"_");

     for (p = this->deletions_byshift; p != NULL; p = List_next(p)) {

       del = (Deletion_T) List_head(p);

-      fprintf(fp,"%s %ld ref:%ld",

+      fprintf(fp,"%s %ld ref:%d",

 	      del->segment,del->count,

 	      deletion_refcount(&refcount_plus,del,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     }

@@ -1341,7 +1341,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_

     fprintf(fp,"x");

     for (p = this->microinvs_byshift; p != NULL; p = List_next(p)) {

       minv = (Microinv_T) List_head(p);

-      fprintf(fp,"%s %ld ref:%ld",

+      fprintf(fp,"%s %ld ref:%d",

 	      minv->segment,minv->count,

 	      minv_refcount(&refcount_plus,minv,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     }

@@ -1360,7 +1360,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_

   }

   if (this->delcounts_plus + this->delcounts_minus > 0) {

-    fprintf(fp," _%ld",this->delcounts_plus + this->delcounts_minus);

+    fprintf(fp," _%d",this->delcounts_plus + this->delcounts_minus);

   }

   return;

@@ -1617,7 +1617,7 @@ print_zeroes (Genomicpos_T start, Genomicpos_T end, char *printchr, int blocksiz

       blockstart = chrpos;

       blockend = chrpos + blocksize;

       if (blockp == true) {

-	printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);

+	printf(">%d %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);

       }

       for (chrpos0 = blockstart; chrpos0 < blockend; chrpos0++) {

 	if (blockp == false) {

@@ -1632,7 +1632,7 @@ print_zeroes (Genomicpos_T start, Genomicpos_T end, char *printchr, int blocksiz

       blockstart = chrpos;

       blockend = end;

       if (blockp == true) {

-	printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);

+	printf(">%d %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);

       }

       for (chrpos0 = blockstart; chrpos0 < blockend; chrpos0++) {

 	if (blockp == false) {

@@ -3772,9 +3772,9 @@ print_softclip_jcns_low (Tally_T this, char *printchr, Genomicpos_T chrpos,

   }

   if (signed_counts_p == false) {

-    printf("%ld",count_plus + count_minus);

+    printf("%d",count_plus + count_minus);

   } else {

-    printf("%ld|%ld",count_plus,count_minus);

+    printf("%d|%d",count_plus,count_minus);

   }

   if (print_cycles_p == true) {

@@ -3826,9 +3826,9 @@ print_softclip_jcns_high (Tally_T this, char *printchr, Genomicpos_T chrpos,

   }

   if (signed_counts_p == false) {

-    printf("%ld",count_plus + count_minus);

+    printf("%d",count_plus + count_minus);

   } else {

-    printf("%ld|%ld",count_plus,count_minus);

+    printf("%d|%d",count_plus,count_minus);

   }

   if (print_cycles_p == true) {

@@ -4036,10 +4036,10 @@ print_insertions (Tally_T this, char *printchr, Genomicpos_T chrpos,

       }

     }

     if (signed_counts_p == false) {

-      printf(" ref:%ld",insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

+      printf(" ref:%d",insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     } else {

       refcount = insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);

-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);

+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);

     }

   }

@@ -4255,10 +4255,10 @@ print_deletions (Tally_T this, char *printchr, Genomicpos_T chrpos,

       }

     }

     if (signed_counts_p == false) {

-      printf(" ref:%ld",deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

+      printf(" ref:%d",deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     } else {

       refcount = deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);

-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);

+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);

     }

   }

@@ -4475,10 +4475,10 @@ print_microinversions (Tally_T this, char *printchr, Genomicpos_T chrpos,

     }

     if (signed_counts_p == false) {

-      printf(" ref:%ld",minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

+      printf(" ref:%d",minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));

     } else {

       refcount = minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);

-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);

+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);

     }

   }

@@ -4545,10 +4545,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches

       for (shift = 0; shift <= this->max_byshift_minus; shift++) {

 	if (this->matches_byshift_minus[shift] > 0) {

 	  if (firstp == true) {

-	    printf("(%ld@%d",this->matches_byshift_minus[shift],-shift);

+	    printf("(%d@%d",this->matches_byshift_minus[shift],-shift);

 	    firstp = false;

 	  } else {

-	    printf(",%ld@%d",this->matches_byshift_minus[shift],-shift);

+	    printf(",%d@%d",this->matches_byshift_minus[shift],-shift);

 	  }

 	  this->matches_byshift_minus[shift] = 0; /* clear */

 	}

@@ -4556,10 +4556,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches

       for (shift = this->max_byshift_plus; shift >= 0; shift--) {

 	if (this->matches_byshift_plus[shift] > 0) {

 	  if (firstp == true) {

-	    printf("(%ld@%d",this->matches_byshift_plus[shift],shift);

+	    printf("(%d@%d",this->matches_byshift_plus[shift],shift);

 	    firstp = false;

 	  } else {

-	    printf(",%ld@%d",this->matches_byshift_plus[shift],shift);

+	    printf(",%d@%d",this->matches_byshift_plus[shift],shift);

 	  }

 	  this->matches_byshift_plus[shift] = 0; /* clear */

 	}

@@ -4588,10 +4588,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches

       for (nm = 0; nm <= this->max_nm; nm++) {

 	if (this->matches_bynm[nm] > 0) {

 	  if (firstp == true) {

-	    printf("(%ldNM%d",this->matches_bynm[nm],nm);

+	    printf("(%dNM%d",this->matches_bynm[nm],nm);

 	    firstp = false;

 	  } else {

-	    printf(",%ldNM%d",this->matches_bynm[nm],nm);

+	    printf(",%dNM%d",this->matches_bynm[nm],nm);

 	  }

 	  this->matches_bynm[nm] = 0; /* clear */

 	}

@@ -4633,10 +4633,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches

       for (xs = 0; xs < 3; xs++) {

 	if (this->matches_byxs[xs] > 0) {

 	  if (firstp == true) {

-	    printf("(%ldXS",this->matches_byxs[xs]);

+	    printf("(%dXS",this->matches_byxs[xs]);

 	    firstp = false;

 	  } else {

-	    printf(",%ldXS",this->matches_byxs[xs]);

+	    printf(",%dXS",this->matches_byxs[xs]);

 	  }

 	  switch (xs) {

 	  case 0: printf("0"); break;

new file mode 100644

@@ -0,0 +1,70 @@

+static char rcsid[] = "$Id: expr.c 206180 2017-05-11 20:34:12Z twu $";

+#ifdef HAVE_CONFIG_H

+#include <config.h>

+#endif

+

+#include "expr.h"

+#include <stdio.h>		/* For sprintf */

+#include <stdlib.h>

+#include "mem.h"

+

+#define T Expr_T

+

+struct T {

+  Genomicpos_T chrpos;

+  long int total;

+  Intlist_T acclist;

+  Intlist_T exonlist;

+  Intlist_T ntlist;

+};

+

+

+void

+Expr_free (T *old) {

+  Intlist_free(&(*old)->acclist);

+  Intlist_free(&(*old)->exonlist);

+  Intlist_free(&(*old)->ntlist);

+

+  FREE(*old);

+  return;

+}

+

+

+T

+Expr_new (Genomicpos_T chrpos, long int total, Intlist_T acclist, Intlist_T exonlist, Intlist_T ntlist) {

+  T new = (T) MALLOC(sizeof(*new));

+

+  new->chrpos = chrpos;

+  new->total = total;

+  new->acclist = acclist;

+  new->exonlist = exonlist;

+  new->ntlist = ntlist;

+

+  return new;

+}

+

+Genomicpos_T

+Expr_chrpos (T this) {

+  return this->chrpos;

+}

+

+long int

+Expr_total (T this) {

+  return this->total;

+}

+

+Intlist_T

+Expr_acclist (T this) {

+  return this->acclist;

+}

+

+Intlist_T

+Expr_exonlist (T this) {

+  return this->exonlist;

+}

+

+Intlist_T

+Expr_ntlist (T this) {

+  return this->ntlist;

+}

+

new file mode 100644

@@ -0,0 +1,28 @@

+/* $Id: expr.h 206180 2017-05-11 20:34:12Z twu $ */

+#ifndef EXPR_INCLUDED

+#define EXPR_INCLUDED

+#include "intlist.h"

+#include "genomicpos.h"

+

+#define T Expr_T

+typedef struct T *T;

+

+extern void

+Expr_free (T *old);

+extern T

+Expr_new (Genomicpos_T chrpos, long int total, Intlist_T acclist, Intlist_T exonlist, Intlist_T ntlist);

+

+extern Genomicpos_T

+Expr_chrpos (T this);

+extern long int

+Expr_total (T this);

+extern Intlist_T

+Expr_acclist (T this);

+extern Intlist_T

+Expr_exonlist (T this);

+extern Intlist_T

+Expr_ntlist (T this);

+

+

+#undef T

+#endif

new file mode 100644

@@ -0,0 +1,150 @@

+static char rcsid[] = "$Id: getline.c 219286 2019-05-21 01:03:23Z twu $";

+

+/* #define STANDALONE 1 */

+

+#include "getline.h"

+

+#include <stdlib.h>

+#include <string.h>		/* For memcpy */

+#include <strings.h>		/* For rindex */

+

+#ifdef STANDALONE

+#define MALLOC malloc

+#define FREE free

+#else

+#include "mem.h"

+#endif

+

+

+#define BUFSIZE 1024

+

+/* Reads arbitrarily long lines from fp.  Strips the '\n' character from the end */

+char *

+Getline (FILE *fp) {

+  size_t size, length;

+  char *buffer, *ptr;

+

+  size = BUFSIZE;

+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));

+  if (fgets(buffer,BUFSIZE,fp) == NULL) {

+    FREE(buffer);

+    return (char *) NULL;

+

+  } else {

+    length = strlen(buffer);

+    while (!feof(fp) && buffer[length-1] != '\n') {

+      size += BUFSIZE;

+

+      ptr = buffer;

+      buffer = (char *) MALLOC(size*sizeof(char));

+      memcpy(buffer,ptr,length*sizeof(char));

+      FREE(ptr);

+

+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);

+      length += strlen(ptr);

+    }

+

+    if (buffer[length-1] == '\n') {

+      buffer[length-1] = '\0';

+      length -= 1;

+    }

+

+    return buffer;

+  }

+}

+

+/* length does not include the "\n" character */

+char *

+Getline_wlength (int *string_length, FILE *fp) {

+  size_t size, length;

+  char *buffer, *ptr;

+

+  size = BUFSIZE;

+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));

+  if (fgets(buffer,BUFSIZE,fp) == NULL) {

+    FREE(buffer);

+    *string_length = 0;

+    return (char *) NULL;

+

+  } else {

+    length = strlen(buffer);

+    while (!feof(fp) && buffer[length-1] != '\n') {

+      size += BUFSIZE;

+

+      ptr = buffer;

+      buffer = (char *) MALLOC(size*sizeof(char));

+      memcpy(buffer,ptr,length*sizeof(char));

+      FREE(ptr);

+

+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);

+      length += strlen(ptr);

+    }

+

+    if (buffer[length-1] == '\n') {

+      buffer[length-1] = '\0';

+      length -= 1;

+    }

+

+    *string_length = length;

+    return buffer;

+  }

+}

+

+

+/* Reads arbitrarily long lines from fp.  Does not strip the '\n'

+   character from the end.  Can be used if we want to reproduce the

+   input file exactly. */

+char *

+Getline_wlinefeed (FILE *fp) {

+  size_t size, length;

+  char *buffer, *ptr;

+

+  size = BUFSIZE;

+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));

+  if (fgets(buffer,BUFSIZE,fp) == NULL) {

+    FREE(buffer);

+    return (char *) NULL;

+

+  } else {

+    length = strlen(buffer);

+    while (!feof(fp) && buffer[length-1] != '\n') {

+      size += BUFSIZE;

+

+      ptr = buffer;

+      buffer = (char *) MALLOC(size*sizeof(char));

+      memcpy(buffer,ptr,length*sizeof(char));

+      FREE(ptr);

+

+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);

+      length += strlen(ptr);

+    }

+

+#if 0

+    if (buffer[length-1] == '\n') {

+      buffer[length-1] = '\0';

+      length -= 1;

+    }

+#endif

+

+    return buffer;

+  }

+}

+

+

+#ifdef STANDALONE

+int

+main (int argc, char *argv[]) {

+  FILE *fp;

+  char *line;

+  int length;

+

+  fp = fopen(argv[1],"r");

+  while ((line = Getline_wlength(&length,fp)) != NULL) {

+    printf("%d: %s\n",length,line);

+    FREE(line);

+  }

+  fclose(fp);

+

+  return 0;

+}

+#endif

new file mode 100644

@@ -0,0 +1,15 @@

+#ifndef GETLINE_INCLUDED

+#define GETLINE_INCLUDED

+

+#include <stdio.h>

+

+extern char *

+Getline (FILE *fp);

+extern char *

+Getline_wlength (int *string_length, FILE *fp);

+extern char *

+Getline_wlinefeed (FILE *fp);

+

+#endif

+

+

@@ -1,4 +1,4 @@

-/* $Id: samflags.h 106634 2013-09-03 17:01:14Z twu $ */

+/* $Id: samflags.h 219289 2019-05-21 01:13:18Z twu $ */

 #ifndef SAMFLAGS_INCLUDED