Browse code

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
Showing17 changed files

... ...
@@ -116,3 +116,4 @@ src/gstruct/src/stamp-h1
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 inst/user
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 inst/usr
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 /src/samtools/libbam.a
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+/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
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.27.1
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+Version: 1.27.2
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2)
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 Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1),
... ...
@@ -17,9 +17,11 @@ setClass("BamTallyParam",
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                         ignore_duplicates = "logical",
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                         min_depth = "integer",
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                         variant_strand = "integer",
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+                        variant_pct = "numeric",
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                         ignore_query_Ns = "logical",
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                         indels = "logical",
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-                        include_soft_clips = "integer",
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+                        min_softclip = "integer",
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+                        max_softclip = "integer",
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                         exon_iit = "character_OR_NULL",
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                         xs = "logical",
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                         read_pos = "logical",
... ...
@@ -103,9 +105,9 @@ BamTallyParam <- function(genome, which = GRanges(),
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                           desired_read_group = NULL, minimum_mapq = 0L,
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                           concordant_only = FALSE, unique_only = FALSE,
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                           primary_only = FALSE, ignore_duplicates = FALSE,
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-                          min_depth = 0L, variant_strand = 0L,
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+                          min_depth = 0L, variant_strand = 0L, variant_pct = 0,
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                           ignore_query_Ns = FALSE,
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-                          indels = FALSE, include_soft_clips = 0L,
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+                          indels = FALSE, min_softclip = 0L, max_softclip = 0L,
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                           exon_iit = NULL, IIT_BPPARAM = NULL,
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                           xs = FALSE, read_pos = FALSE,
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                           min_base_quality = 0L, noncovered = FALSE,
... ...
@@ -127,12 +129,18 @@ BamTallyParam <- function(genome, which = GRanges(),
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     stop("min_depth must be a single, non-negative, non-NA number")
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   if (!variant_strand %in% c(0, 1, 2))
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     stop("variant_strand must be one of 0, 1, or 2")
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+  if (variant_pct < 0)
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+    stop("variant_pct must be non-negative")
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   if (!isTRUEorFALSE(ignore_query_Ns))
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     stop("ignore_query_Ns must be TRUE or FALSE")
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   if (!isTRUEorFALSE(indels))
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     stop("indels must be TRUE or FALSE")
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-  if (include_soft_clips < 0)
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-    stop("include_soft_clips must be non-negative")
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+  if (max_softclip < 0L)
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+    stop("max_softclip must be non-negative")
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+  if (min_softclip < 0L)
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+    stop("min_softclip must be non-negative")
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+  if (max_softclip < min_softclip)
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+    stop("max_softclip must be at least equal to min_softclip")
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   if (!isTRUEorFALSE(xs))
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     stop("xs must be TRUE or FALSE")
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   if (!isTRUEorFALSE(read_pos))
... ...
@@ -149,7 +157,7 @@ BamTallyParam <- function(genome, which = GRanges(),
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   params$which <- normArgWhich(which, params$genome)
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   params$exon_iit = normArgCdsIIT(params$exon_iit, BPPARAM = IIT_BPPARAM)
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   integer_params <- c("minimum_mapq", "min_depth", "variant_strand",
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-                      "include_soft_clips")
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+                      "min_softclip", "max_softclip")
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   params[integer_params] <- lapply(params[integer_params], as.integer)
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   params = params[names(params) != "IIT_BPPARAM"]
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   do.call(new, c("BamTallyParam", params))  
... ...
@@ -205,6 +205,13 @@ normArgSingleInteger <- function(x) {
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     stop("'", name, "' should be a single, non-NA integer")
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   x
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 }
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+normArgSingleNumber <- function(x) {
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+    name <- deparse(substitute(x))
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+    x <- as.numeric(x)
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+    if (!isSingleNumber(x))
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+        stop("'", name, "' should be a single, non-NA number")
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+    x
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+}
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 normArgTRUEorFALSE <- function(x) {
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   name <- deparse(substitute(x))
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   if (!isTRUEorFALSE(x))
... ...
@@ -227,11 +234,11 @@ normArgSingleCharacterOrNULL <- function(x) {
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                          maximum_nhits = 1000000L,
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                          concordant_only = FALSE, unique_only = FALSE,
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                          primary_only = FALSE, ignore_duplicates = FALSE,
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-                         min_depth = 0L, variant_strand = 0L,
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+                         min_depth = 0L, variant_strand = 0L, variant_pct = 0,
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                          ignore_query_Ns = FALSE,
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                          indels = FALSE,
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                          blocksize = 1000L, verbosep = FALSE,
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-                         include_soft_clips = 0L,
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+                         min_softclip = 0L, max_softclip = 0L,
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                          exon_iit = NULL, xs = FALSE, read_pos = FALSE,
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                          min_base_quality = 0L, noncovered = FALSE, nm = FALSE)
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 {
... ...
@@ -258,11 +265,13 @@ normArgSingleCharacterOrNULL <- function(x) {
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         normArgTRUEorFALSE(ignore_duplicates),
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         normArgSingleInteger(min_depth),
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         normArgSingleInteger(variant_strand),
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+        normArgSingleNumber(variant_pct),
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         normArgTRUEorFALSE(ignore_query_Ns),
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         normArgTRUEorFALSE(indels),
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         normArgSingleInteger(blocksize),
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         normArgTRUEorFALSE(verbosep),
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-        normArgSingleInteger(include_soft_clips),
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+        normArgSingleInteger(min_softclip),
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+        normArgSingleInteger(max_softclip),
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         normArgSingleCharacterOrNULL(exon_iit),
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         normArgTRUEorFALSE(xs),
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         normArgTRUEorFALSE(read_pos),
... ...
@@ -8,9 +8,9 @@ test_BamTallyParam <- function() {
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                minimum_mapq = 0L,
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                concordant_only = FALSE, unique_only = FALSE,
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                primary_only = FALSE, ignore_duplicates = FALSE,
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-               min_depth = 0L, variant_strand = 0L,
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+               min_depth = 0L, variant_strand = 0L, variant_pct = 0,
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                ignore_query_Ns = FALSE,
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-               indels = FALSE, include_soft_clips = 0L,
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+               indels = FALSE, min_softclip = 0L, max_softclip = 0L,
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                xs = FALSE, read_pos = FALSE, min_base_quality = 0L,
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                noncovered = FALSE, nm = FALSE)
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   which <- TP53Which()
... ...
@@ -19,9 +19,9 @@
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                 minimum_mapq = 0L,
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                 concordant_only = FALSE, unique_only = FALSE,
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                 primary_only = FALSE, ignore_duplicates = FALSE,
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-                min_depth = 0L, variant_strand = 0L,
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+                min_depth = 0L, variant_strand = 0L, variant_pct = 0,
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                 ignore_query_Ns = FALSE,
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-                indels = FALSE, include_soft_clips = 0L,
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+                indels = FALSE, min_softclip = 0L, max_softclip = 0L,
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                 exon_iit = NULL, IIT_BPPARAM = NULL,
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                 xs = FALSE, read_pos = FALSE,
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                 min_base_quality = 0L, noncovered = FALSE, nm = FALSE)
... ...
@@ -52,6 +52,8 @@
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     only positions where a variant was seen on at least one strand, and
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     2 requires the variant be seen on both strands. Setting this to 1
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     is a good way to save resources.}
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+  \item{variant_pct}{The minimum alternate allele fraction
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+    for a variant to be reported for a strand.} 
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   \item{ignore_query_Ns}{Whether to ignore the N base pairs when
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     counting. Can save a lot of resources when processing low quality data.}
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   \item{indels}{Whether to return indel counts. The \code{ref} and
... ...
@@ -60,7 +62,8 @@
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     always spans the sequence in \code{ref}; so e.g. a deletion extends
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     one nt upstream of the actual deleted sequence.
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   }
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-  \item{include_soft_clips}{Maximum length of soft clips that are
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+  \item{min_softclip, max_softclip}{
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+    Minimum and maximum length of soft clips that are
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     considered for counting. Soft-clipping is often useful (for GSNAP at
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     least) during alignment, and it should be preserved in the
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     output. However, soft clipping can preferentially occur in regions
... ...
@@ -7,7 +7,7 @@
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 static const R_CallMethodDef callMethods[] = {
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   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 26),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 28),
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   CALLMETHOD_DEF(R_tally_iit_parse, 6),
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   /* bamreader.c */
... ...
@@ -19,11 +19,11 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
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                 SEXP maximum_nhits_R,
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                 SEXP need_concordant_p_R, SEXP need_unique_p_R,
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                 SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,
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-                SEXP min_depth_R, SEXP variant_strands_R,
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+                SEXP min_depth_R, SEXP variant_strands_R, SEXP variant_pct_R,
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                 SEXP ignore_query_Ns_p_R,
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                 SEXP print_indels_p_R,
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                 SEXP blocksize_R, 
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-                SEXP verbosep_R, SEXP max_softclip_R,
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+                SEXP verbosep_R, SEXP min_softclip_R, SEXP max_softclip_R,
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                 SEXP exon_iit_file_R,
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                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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                 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,
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     genome_dir_R == R_NilValue ? NULL : CHAR(asChar(genome_dir_R));
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   const char *db = CHAR(asChar(db_R));
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   int alloclength = asInteger(alloclength_R);
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+  int pastlength = alloclength;
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   const char *desired_read_group =
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     desired_read_group_R == R_NilValue ? NULL :
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     CHAR(asChar(desired_read_group_R));
... ...
@@ -46,10 +47,12 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
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   bool ignore_duplicates_p = asLogical(ignore_duplicates_p_R);
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   int min_depth = asInteger(min_depth_R);
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   int variant_strands = asInteger(variant_strands_R);
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+  double variant_pct = asReal(variant_pct_R);
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   bool ignore_query_Ns_p = asLogical(ignore_query_Ns_p_R);
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   bool print_indels_p = asLogical(print_indels_p_R);
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   int blocksize = asInteger(blocksize_R);
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   int verbosep = asLogical(verbosep_R);
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+  int min_softclip = asInteger(min_softclip_R);
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   int max_softclip = asInteger(max_softclip_R);
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   bool print_xs_scores_p = asLogical(print_xs_scores_p_R);
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   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,
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                                  genome,
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                                  chromosome_iit,
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                                  map_iit,
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-                                 alloclength,
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+                                 alloclength, pastlength,
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                                  (char *)desired_read_group,
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                                  minimum_mapq, good_unique_mapq,
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                                  minimum_quality_score,
... ...
@@ -87,10 +90,11 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
87 90
                                  need_unique_p, need_primary_p,
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                                  ignore_duplicates_p,
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                                  min_depth, variant_strands,
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-				 /* TODO: variant_pct */ 0,
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+				 variant_pct,
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 				 ignore_query_Ns_p,
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                                  print_indels_p, blocksize, verbosep,
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-                                 /*readlevel_p*/false, max_softclip,
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+                                 /*readlevel_p*/false,
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+				 min_softclip, max_softclip,
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                                  print_cycles_p,
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                                  print_nm_scores_p,
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                                  print_xs_scores_p, noncovered_p);
... ...
@@ -16,14 +16,14 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
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                 SEXP maximum_nhits_R,
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                 SEXP need_concordant_p_R, SEXP need_unique_p_R,
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                 SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,
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-                SEXP min_depth_R, SEXP variant_strands_R,
20
-                SEXP ignore_query_Ns_p,
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+                SEXP min_depth_R, SEXP variant_strands_R, SEXP variant_pct_R,
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+                SEXP ignore_query_Ns_p_R,
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                 SEXP print_indels_p_R,
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                 SEXP blocksize_R, 
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-                SEXP verbosep_R, SEXP max_softclip_R,
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-                SEXP genome_iit_file_R,
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+                SEXP verbosep_R, SEXP min_softclip_R, SEXP max_softclip_R,
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+                SEXP exon_iit_file_R,
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                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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-                SEXP minimum_quality_score_R, SEXP nonconvered_R,
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+                SEXP minimum_quality_score_R, SEXP noncovered_R,
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                 SEXP print_nm_scores_p_R);
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29 29
 SEXP
... ...
@@ -23,12 +23,12 @@ BAM_TALLY_FILES = fopen.h bool.h types.h bam.h bgzf.h \
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  md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \
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  uinttable.c uinttable.h table.c table.h \
25 25
  chrnum.c chrnum.h \
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- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
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+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
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  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
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  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
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- translation.c translation.h bamtally.c bamtally.h \
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+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
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  datadir.c datadir.h \
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- getopt.c getopt1.c getopt.h bamtally_main.c
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+ getline.c getline.h getopt.c getopt1.c getopt.h bamtally_main.c
32 32
 
33 33
 if HAVE_SAMTOOLS_LIB
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 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 \
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  md5.c md5.h sequence.c sequence.h genome.c genome.h \
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  uinttable.c uinttable.h table.c table.h \
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  chrnum.c chrnum.h \
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- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
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+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
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  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
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  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
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- translation.c translation.h bamtally.c bamtally.h \
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+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
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  datadir.c datadir.h
56 56
 
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 # Do not add SAMTOOLS LIBS here
... ...
@@ -167,12 +167,12 @@ am__dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES_DIST =  \
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 	iit-read.c iit-read.h complement.h chrom.c chrom.h \
168 168
 	genomicpos.c genomicpos.h md5.c md5.h sequence.c sequence.h \
169 169
 	genome.c genome.h uinttable.c uinttable.h table.c table.h \
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-	chrnum.c chrnum.h bamread.c bamread.h samread.c samread.h \
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-	parserange.c parserange.h tableuint.c tableuint.h iit-write.c \
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-	iit-write.h ucharlist.c ucharlist.h matchdef.h matchpool.c \
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-	matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h \
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-	tally.c tally.h translation.c translation.h bamtally.c \
175
-	bamtally.h datadir.c datadir.h
170
+	chrnum.c chrnum.h samflags.h bamread.c bamread.h samread.c \
171
+	samread.h parserange.c parserange.h tableuint.c tableuint.h \
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+	iit-write.c iit-write.h ucharlist.c ucharlist.h matchdef.h \
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+	matchpool.c matchpool.h mismatchdef.h mismatchpool.c \
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+	mismatchpool.h tally.c tally.h translation.c translation.h \
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+	expr.c expr.h bamtally.c bamtally.h datadir.c datadir.h
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 am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \
177 177
 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-assert.lo \
178 178
 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mem.lo \
... ...
@@ -203,6 +203,7 @@ am__objects_1 = libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.lo \
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 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.lo \
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 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-tally.lo \
205 205
 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.lo \
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+	libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo \
206 207
 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo \
207 208
 	libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.lo
208 209
 @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 \
228 229
 	access.h iitdef.h iit-read.c iit-read.h chrom.c chrom.h \
229 230
 	genomicpos.c genomicpos.h md5.c md5.h complement.h sequence.c \
230 231
 	sequence.h genome.c genome.h uinttable.c uinttable.h table.c \
231
-	table.h chrnum.c chrnum.h bamread.c bamread.h samread.c \
232
-	samread.h parserange.c parserange.h tableuint.c tableuint.h \
233
-	iit-write.c iit-write.h ucharlist.c ucharlist.h matchdef.h \
234
-	matchpool.c matchpool.h mismatchdef.h mismatchpool.c \
235
-	mismatchpool.h tally.c tally.h translation.c translation.h \
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-	bamtally.c bamtally.h datadir.c datadir.h getopt.c getopt1.c \
237
-	getopt.h bamtally_main.c
232
+	table.h chrnum.c chrnum.h samflags.h bamread.c bamread.h \
233
+	samread.c samread.h parserange.c parserange.h tableuint.c \
234
+	tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
235
+	matchdef.h matchpool.c matchpool.h mismatchdef.h \
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+	mismatchpool.c mismatchpool.h tally.c tally.h translation.c \
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+	translation.h expr.c expr.h bamtally.c bamtally.h datadir.c \
238
+	datadir.h getline.c getline.h getopt.c getopt1.c getopt.h \
239
+	bamtally_main.c
238 240
 am__objects_2 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \
239 241
 	bam_tally-mem.$(OBJEXT) bam_tally-intlist.$(OBJEXT) \
240 242
 	bam_tally-list.$(OBJEXT) bam_tally-littleendian.$(OBJEXT) \
... ...
@@ -250,7 +252,8 @@ am__objects_2 = bam_tally-except.$(OBJEXT) bam_tally-assert.$(OBJEXT) \
250 252
 	bam_tally-iit-write.$(OBJEXT) bam_tally-ucharlist.$(OBJEXT) \
251 253
 	bam_tally-matchpool.$(OBJEXT) bam_tally-mismatchpool.$(OBJEXT) \
252 254
 	bam_tally-tally.$(OBJEXT) bam_tally-translation.$(OBJEXT) \
253
-	bam_tally-bamtally.$(OBJEXT) bam_tally-datadir.$(OBJEXT) \
255
+	bam_tally-expr.$(OBJEXT) bam_tally-bamtally.$(OBJEXT) \
256
+	bam_tally-datadir.$(OBJEXT) bam_tally-getline.$(OBJEXT) \
254 257
 	bam_tally-getopt.$(OBJEXT) bam_tally-getopt1.$(OBJEXT) \
255 258
 	bam_tally-bamtally_main.$(OBJEXT)
256 259
 @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 \
492 495
  md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \
493 496
  uinttable.c uinttable.h table.c table.h \
494 497
  chrnum.c chrnum.h \
495
- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
498
+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
496 499
  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
497 500
  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
498
- translation.c translation.h bamtally.c bamtally.h \
501
+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
499 502
  datadir.c datadir.h \
500
- getopt.c getopt1.c getopt.h bamtally_main.c
503
+ getline.c getline.h getopt.c getopt1.c getopt.h bamtally_main.c
501 504
 
502 505
 @HAVE_SAMTOOLS_LIB_TRUE@bam_tally_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_CFLAGS) $(POPCNT_FLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
503 506
 @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 \
513 516
  md5.c md5.h sequence.c sequence.h genome.c genome.h \
514 517
  uinttable.c uinttable.h table.c table.h \
515 518
  chrnum.c chrnum.h \
516
- bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
519
+ samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
517 520
  tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
518 521
  matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
519
- translation.c translation.h bamtally.c bamtally.h \
522
+ translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
520 523
  datadir.c datadir.h
521 524
 
522 525
 
... ...
@@ -707,8 +710,10 @@ distclean-compile:
707 710
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrom.Po@am__quote@
708 711
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-datadir.Po@am__quote@
709 712
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-except.Po@am__quote@
713
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-expr.Po@am__quote@
710 714
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genome.Po@am__quote@
711 715
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genomicpos.Po@am__quote@
716
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getline.Po@am__quote@
712 717
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt.Po@am__quote@
713 718
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt1.Po@am__quote@
714 719
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-iit-read.Po@am__quote@
... ...
@@ -741,6 +746,7 @@ distclean-compile:
741 746
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrom.Plo@am__quote@
742 747
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.Plo@am__quote@
743 748
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.Plo@am__quote@
749
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Plo@am__quote@
744 750
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genome.Plo@am__quote@
745 751
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genomicpos.Plo@am__quote@
746 752
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-iit-read.Plo@am__quote@
... ...
@@ -996,6 +1002,13 @@ libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.lo: translation.c
996 1002
 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
997 1003
 @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
998 1004
 
1005
+libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo: expr.c
1006
+@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
1007
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Tpo $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Plo
1008
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.lo' libtool=yes @AMDEPBACKSLASH@
1009
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1010
+@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
1011
+
999 1012
 libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.lo: bamtally.c
1000 1013
 @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
1001 1014
 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Tpo $(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Plo
... ...
@@ -1430,6 +1443,20 @@ bam_tally-translation.obj: translation.c
1430 1443
 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1431 1444
 @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`
1432 1445
 
1446
+bam_tally-expr.o: expr.c
1447
+@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
1448
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-expr.Tpo $(DEPDIR)/bam_tally-expr.Po
1449
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='bam_tally-expr.o' libtool=no @AMDEPBACKSLASH@
1450
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1451
+@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
1452
+
1453
+bam_tally-expr.obj: expr.c
1454
+@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`
1455
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-expr.Tpo $(DEPDIR)/bam_tally-expr.Po
1456
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='expr.c' object='bam_tally-expr.obj' libtool=no @AMDEPBACKSLASH@
1457
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1458
+@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`
1459
+
1433 1460
 bam_tally-bamtally.o: bamtally.c
1434 1461
 @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
1435 1462
 @am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-bamtally.Tpo $(DEPDIR)/bam_tally-bamtally.Po
... ...
@@ -1458,6 +1485,20 @@ bam_tally-datadir.obj: datadir.c
1458 1485
 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1459 1486
 @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`
1460 1487
 
1488
+bam_tally-getline.o: getline.c
1489
+@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
1490
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-getline.Tpo $(DEPDIR)/bam_tally-getline.Po
1491
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='getline.c' object='bam_tally-getline.o' libtool=no @AMDEPBACKSLASH@
1492
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1493
+@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
1494
+
1495
+bam_tally-getline.obj: getline.c
1496
+@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`
1497
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/bam_tally-getline.Tpo $(DEPDIR)/bam_tally-getline.Po
1498
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='getline.c' object='bam_tally-getline.obj' libtool=no @AMDEPBACKSLASH@
1499
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
1500
+@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`
1501
+
1461 1502
 bam_tally-getopt.o: getopt.c
1462 1503
 @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
1463 1504
 @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_
1317 1317
     fprintf(fp,"^");
1318 1318
     for (p = this->insertions_byshift; p != NULL; p = List_next(p)) {
1319 1319
       ins = (Insertion_T) List_head(p);
1320
-      fprintf(fp,"%s %ld ref:%ld",
1320
+      fprintf(fp,"%s %ld ref:%d",
1321 1321
 	      ins->segment,ins->count,
1322 1322
 	      insertion_refcount(&refcount_plus,ins,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
1323 1323
     }
... ...
@@ -1329,7 +1329,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_
1329 1329
     fprintf(fp,"_");
1330 1330
     for (p = this->deletions_byshift; p != NULL; p = List_next(p)) {
1331 1331
       del = (Deletion_T) List_head(p);
1332
-      fprintf(fp,"%s %ld ref:%ld",
1332
+      fprintf(fp,"%s %ld ref:%d",
1333 1333
 	      del->segment,del->count,
1334 1334
 	      deletion_refcount(&refcount_plus,del,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
1335 1335
     }
... ...
@@ -1341,7 +1341,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_
1341 1341
     fprintf(fp,"x");
1342 1342
     for (p = this->microinvs_byshift; p != NULL; p = List_next(p)) {
1343 1343
       minv = (Microinv_T) List_head(p);
1344
-      fprintf(fp,"%s %ld ref:%ld",
1344
+      fprintf(fp,"%s %ld ref:%d",
1345 1345
 	      minv->segment,minv->count,
1346 1346
 	      minv_refcount(&refcount_plus,minv,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
1347 1347
     }
... ...
@@ -1360,7 +1360,7 @@ print_allele_counts_simple (FILE *fp, Tally_T this, Genome_T genome, Genomicpos_
1360 1360
   }
1361 1361
 
1362 1362
   if (this->delcounts_plus + this->delcounts_minus > 0) {
1363
-    fprintf(fp," _%ld",this->delcounts_plus + this->delcounts_minus);
1363
+    fprintf(fp," _%d",this->delcounts_plus + this->delcounts_minus);
1364 1364
   }
1365 1365
 
1366 1366
   return;
... ...
@@ -1617,7 +1617,7 @@ print_zeroes (Genomicpos_T start, Genomicpos_T end, char *printchr, int blocksiz
1617 1617
       blockstart = chrpos;
1618 1618
       blockend = chrpos + blocksize;
1619 1619
       if (blockp == true) {
1620
-	printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
1620
+	printf(">%d %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
1621 1621
       }
1622 1622
       for (chrpos0 = blockstart; chrpos0 < blockend; chrpos0++) {
1623 1623
 	if (blockp == false) {
... ...
@@ -1632,7 +1632,7 @@ print_zeroes (Genomicpos_T start, Genomicpos_T end, char *printchr, int blocksiz
1632 1632
       blockstart = chrpos;
1633 1633
       blockend = end;
1634 1634
       if (blockp == true) {
1635
-	printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
1635
+	printf(">%d %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
1636 1636
       }
1637 1637
       for (chrpos0 = blockstart; chrpos0 < blockend; chrpos0++) {
1638 1638
 	if (blockp == false) {
... ...
@@ -3772,9 +3772,9 @@ print_softclip_jcns_low (Tally_T this, char *printchr, Genomicpos_T chrpos,
3772 3772
   }
3773 3773
 
3774 3774
   if (signed_counts_p == false) {
3775
-    printf("%ld",count_plus + count_minus);
3775
+    printf("%d",count_plus + count_minus);
3776 3776
   } else {
3777
-    printf("%ld|%ld",count_plus,count_minus);
3777
+    printf("%d|%d",count_plus,count_minus);
3778 3778
   }
3779 3779
 
3780 3780
   if (print_cycles_p == true) {
... ...
@@ -3826,9 +3826,9 @@ print_softclip_jcns_high (Tally_T this, char *printchr, Genomicpos_T chrpos,
3826 3826
   }
3827 3827
 
3828 3828
   if (signed_counts_p == false) {
3829
-    printf("%ld",count_plus + count_minus);
3829
+    printf("%d",count_plus + count_minus);
3830 3830
   } else {
3831
-    printf("%ld|%ld",count_plus,count_minus);
3831
+    printf("%d|%d",count_plus,count_minus);
3832 3832
   }
3833 3833
 
3834 3834
   if (print_cycles_p == true) {
... ...
@@ -4036,10 +4036,10 @@ print_insertions (Tally_T this, char *printchr, Genomicpos_T chrpos,
4036 4036
       }
4037 4037
     }
4038 4038
     if (signed_counts_p == false) {
4039
-      printf(" ref:%ld",insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4039
+      printf(" ref:%d",insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4040 4040
     } else {
4041 4041
       refcount = insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);
4042
-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
4042
+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);
4043 4043
     }
4044 4044
   }
4045 4045
 
... ...
@@ -4255,10 +4255,10 @@ print_deletions (Tally_T this, char *printchr, Genomicpos_T chrpos,
4255 4255
       }
4256 4256
     }
4257 4257
     if (signed_counts_p == false) {
4258
-      printf(" ref:%ld",deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4258
+      printf(" ref:%d",deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4259 4259
     } else {
4260 4260
       refcount = deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);
4261
-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
4261
+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);
4262 4262
     }
4263 4263
   }
4264 4264
 
... ...
@@ -4475,10 +4475,10 @@ print_microinversions (Tally_T this, char *printchr, Genomicpos_T chrpos,
4475 4475
     }
4476 4476
 
4477 4477
     if (signed_counts_p == false) {
4478
-      printf(" ref:%ld",minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4478
+      printf(" ref:%d",minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip));
4479 4479
     } else {
4480 4480
       refcount = minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,min_softclip,max_softclip);
4481
-      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
4481
+      printf(" ref:%d|%d",refcount_plus,refcount - refcount_plus);
4482 4482
     }
4483 4483
   }
4484 4484
 
... ...
@@ -4545,10 +4545,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches
4545 4545
       for (shift = 0; shift <= this->max_byshift_minus; shift++) {
4546 4546
 	if (this->matches_byshift_minus[shift] > 0) {
4547 4547
 	  if (firstp == true) {
4548
-	    printf("(%ld@%d",this->matches_byshift_minus[shift],-shift);
4548
+	    printf("(%d@%d",this->matches_byshift_minus[shift],-shift);
4549 4549
 	    firstp = false;
4550 4550
 	  } else {
4551
-	    printf(",%ld@%d",this->matches_byshift_minus[shift],-shift);
4551
+	    printf(",%d@%d",this->matches_byshift_minus[shift],-shift);
4552 4552
 	  }
4553 4553
 	  this->matches_byshift_minus[shift] = 0; /* clear */
4554 4554
 	}
... ...
@@ -4556,10 +4556,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches
4556 4556
       for (shift = this->max_byshift_plus; shift >= 0; shift--) {
4557 4557
 	if (this->matches_byshift_plus[shift] > 0) {
4558 4558
 	  if (firstp == true) {
4559
-	    printf("(%ld@%d",this->matches_byshift_plus[shift],shift);
4559
+	    printf("(%d@%d",this->matches_byshift_plus[shift],shift);
4560 4560
 	    firstp = false;
4561 4561
 	  } else {
4562
-	    printf(",%ld@%d",this->matches_byshift_plus[shift],shift);
4562
+	    printf(",%d@%d",this->matches_byshift_plus[shift],shift);
4563 4563
 	  }
4564 4564
 	  this->matches_byshift_plus[shift] = 0; /* clear */
4565 4565
 	}
... ...
@@ -4588,10 +4588,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches
4588 4588
       for (nm = 0; nm <= this->max_nm; nm++) {
4589 4589
 	if (this->matches_bynm[nm] > 0) {
4590 4590
 	  if (firstp == true) {
4591
-	    printf("(%ldNM%d",this->matches_bynm[nm],nm);
4591
+	    printf("(%dNM%d",this->matches_bynm[nm],nm);
4592 4592
 	    firstp = false;
4593 4593
 	  } else {
4594
-	    printf(",%ldNM%d",this->matches_bynm[nm],nm);
4594
+	    printf(",%dNM%d",this->matches_bynm[nm],nm);
4595 4595
 	  }
4596 4596
 	  this->matches_bynm[nm] = 0; /* clear */
4597 4597
 	}
... ...
@@ -4633,10 +4633,10 @@ print_matches (Tally_T this, long int total_matches_plus, long int total_matches
4633 4633
       for (xs = 0; xs < 3; xs++) {
4634 4634
 	if (this->matches_byxs[xs] > 0) {
4635 4635
 	  if (firstp == true) {
4636
-	    printf("(%ldXS",this->matches_byxs[xs]);
4636
+	    printf("(%dXS",this->matches_byxs[xs]);
4637 4637
 	    firstp = false;
4638 4638
 	  } else {
4639
-	    printf(",%ldXS",this->matches_byxs[xs]);
4639
+	    printf(",%dXS",this->matches_byxs[xs]);
4640 4640
 	  }
4641 4641
 	  switch (xs) {
4642 4642
 	  case 0: printf("0"); break;
4643 4643
new file mode 100644
... ...
@@ -0,0 +1,70 @@
1
+static char rcsid[] = "$Id: expr.c 206180 2017-05-11 20:34:12Z twu $";
2
+#ifdef HAVE_CONFIG_H
3
+#include <config.h>
4
+#endif
5
+
6
+#include "expr.h"
7
+#include <stdio.h>		/* For sprintf */
8
+#include <stdlib.h>
9
+#include "mem.h"
10
+
11
+#define T Expr_T
12
+
13
+struct T {
14
+  Genomicpos_T chrpos;
15
+  long int total;
16
+  Intlist_T acclist;
17
+  Intlist_T exonlist;
18
+  Intlist_T ntlist;
19
+};
20
+
21
+
22
+void
23
+Expr_free (T *old) {
24
+  Intlist_free(&(*old)->acclist);
25
+  Intlist_free(&(*old)->exonlist);
26
+  Intlist_free(&(*old)->ntlist);
27
+
28
+  FREE(*old);
29
+  return;
30
+}
31
+
32
+
33
+T
34
+Expr_new (Genomicpos_T chrpos, long int total, Intlist_T acclist, Intlist_T exonlist, Intlist_T ntlist) {
35
+  T new = (T) MALLOC(sizeof(*new));
36
+
37
+  new->chrpos = chrpos;
38
+  new->total = total;
39
+  new->acclist = acclist;
40
+  new->exonlist = exonlist;
41
+  new->ntlist = ntlist;
42
+
43
+  return new;
44
+}
45
+
46
+Genomicpos_T
47
+Expr_chrpos (T this) {
48
+  return this->chrpos;
49
+}
50
+
51
+long int
52
+Expr_total (T this) {
53
+  return this->total;
54
+}
55
+
56
+Intlist_T
57
+Expr_acclist (T this) {
58
+  return this->acclist;
59
+}
60
+
61
+Intlist_T
62
+Expr_exonlist (T this) {
63
+  return this->exonlist;
64
+}
65
+
66
+Intlist_T
67
+Expr_ntlist (T this) {
68
+  return this->ntlist;
69
+}
70
+
0 71
new file mode 100644
... ...
@@ -0,0 +1,28 @@
1
+/* $Id: expr.h 206180 2017-05-11 20:34:12Z twu $ */
2
+#ifndef EXPR_INCLUDED
3
+#define EXPR_INCLUDED
4
+#include "intlist.h"
5
+#include "genomicpos.h"
6
+
7
+#define T Expr_T
8
+typedef struct T *T;
9
+
10
+extern void
11
+Expr_free (T *old);
12
+extern T
13
+Expr_new (Genomicpos_T chrpos, long int total, Intlist_T acclist, Intlist_T exonlist, Intlist_T ntlist);
14
+
15
+extern Genomicpos_T
16
+Expr_chrpos (T this);
17
+extern long int
18
+Expr_total (T this);
19
+extern Intlist_T
20
+Expr_acclist (T this);
21
+extern Intlist_T
22
+Expr_exonlist (T this);
23
+extern Intlist_T
24
+Expr_ntlist (T this);
25
+
26
+
27
+#undef T
28
+#endif
0 29
new file mode 100644
... ...
@@ -0,0 +1,150 @@
1
+static char rcsid[] = "$Id: getline.c 219286 2019-05-21 01:03:23Z twu $";
2
+
3
+/* #define STANDALONE 1 */
4
+
5
+#include "getline.h"
6
+
7
+#include <stdlib.h>
8
+#include <string.h>		/* For memcpy */
9
+#include <strings.h>		/* For rindex */
10
+
11
+#ifdef STANDALONE
12
+#define MALLOC malloc
13
+#define FREE free
14
+#else
15
+#include "mem.h"
16
+#endif
17
+
18
+
19
+#define BUFSIZE 1024
20
+
21
+/* Reads arbitrarily long lines from fp.  Strips the '\n' character from the end */
22
+char *
23
+Getline (FILE *fp) {
24
+  size_t size, length;
25
+  char *buffer, *ptr;
26
+
27
+  size = BUFSIZE;
28
+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));
29
+  if (fgets(buffer,BUFSIZE,fp) == NULL) {
30
+    FREE(buffer);
31
+    return (char *) NULL;
32
+
33
+  } else {
34
+    length = strlen(buffer);
35
+    while (!feof(fp) && buffer[length-1] != '\n') {
36
+      size += BUFSIZE;
37
+
38
+      ptr = buffer;
39
+      buffer = (char *) MALLOC(size*sizeof(char));
40
+      memcpy(buffer,ptr,length*sizeof(char));
41
+      FREE(ptr);
42
+
43
+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);
44
+      length += strlen(ptr);
45
+    }
46
+
47
+    if (buffer[length-1] == '\n') {
48
+      buffer[length-1] = '\0';
49
+      length -= 1;
50
+    }
51
+
52
+    return buffer;
53
+  }
54
+}
55
+
56
+/* length does not include the "\n" character */
57
+char *
58
+Getline_wlength (int *string_length, FILE *fp) {
59
+  size_t size, length;
60
+  char *buffer, *ptr;
61
+
62
+  size = BUFSIZE;
63
+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));
64
+  if (fgets(buffer,BUFSIZE,fp) == NULL) {
65
+    FREE(buffer);
66
+    *string_length = 0;
67
+    return (char *) NULL;
68
+
69
+  } else {
70
+    length = strlen(buffer);
71
+    while (!feof(fp) && buffer[length-1] != '\n') {
72
+      size += BUFSIZE;
73
+
74
+      ptr = buffer;
75
+      buffer = (char *) MALLOC(size*sizeof(char));
76
+      memcpy(buffer,ptr,length*sizeof(char));
77
+      FREE(ptr);
78
+
79
+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);
80
+      length += strlen(ptr);
81
+    }
82
+
83
+    if (buffer[length-1] == '\n') {
84
+      buffer[length-1] = '\0';
85
+      length -= 1;
86
+    }
87
+
88
+    *string_length = length;
89
+    return buffer;
90
+  }
91
+}
92
+
93
+
94
+/* Reads arbitrarily long lines from fp.  Does not strip the '\n'
95
+   character from the end.  Can be used if we want to reproduce the
96
+   input file exactly. */
97
+char *
98
+Getline_wlinefeed (FILE *fp) {
99
+  size_t size, length;
100
+  char *buffer, *ptr;
101
+
102
+  size = BUFSIZE;
103
+  buffer = (char *) MALLOC(BUFSIZE*sizeof(char));
104
+  if (fgets(buffer,BUFSIZE,fp) == NULL) {
105
+    FREE(buffer);
106
+    return (char *) NULL;
107
+
108
+  } else {
109
+    length = strlen(buffer);
110
+    while (!feof(fp) && buffer[length-1] != '\n') {
111
+      size += BUFSIZE;
112
+
113
+      ptr = buffer;
114
+      buffer = (char *) MALLOC(size*sizeof(char));
115
+      memcpy(buffer,ptr,length*sizeof(char));
116
+      FREE(ptr);
117
+
118
+      ptr = fgets(&(buffer[length]),BUFSIZE,fp);
119
+      length += strlen(ptr);
120
+    }
121
+
122
+#if 0
123
+    if (buffer[length-1] == '\n') {
124
+      buffer[length-1] = '\0';
125
+      length -= 1;
126
+    }
127
+#endif
128
+
129
+    return buffer;
130
+  }
131
+}
132
+
133
+
134
+#ifdef STANDALONE
135
+int
136
+main (int argc, char *argv[]) {
137
+  FILE *fp;
138
+  char *line;
139
+  int length;
140
+
141
+  fp = fopen(argv[1],"r");
142
+  while ((line = Getline_wlength(&length,fp)) != NULL) {
143
+    printf("%d: %s\n",length,line);
144
+    FREE(line);
145
+  }
146
+  fclose(fp);
147
+
148
+  return 0;
149
+}
150
+#endif
0 151
new file mode 100644
... ...
@@ -0,0 +1,15 @@
1
+#ifndef GETLINE_INCLUDED
2
+#define GETLINE_INCLUDED
3
+
4
+#include <stdio.h>
5
+
6
+extern char *
7
+Getline (FILE *fp);
8
+extern char *
9
+Getline_wlength (int *string_length, FILE *fp);
10
+extern char *
11
+Getline_wlinefeed (FILE *fp);
12
+
13
+#endif
14
+
15
+
... ...
@@ -1,4 +1,4 @@
1
-/* $Id: samflags.h 106634 2013-09-03 17:01:14Z twu $ */
1
+/* $Id: samflags.h 219289 2019-05-21 01:13:18Z twu $ */
2 2
 #ifndef SAMFLAGS_INCLUDED
3 3
 #define SAMFLAGS_INCLUDED
4 4
 
... ...
@@ -13,6 +13,7 @@
13 13
 #define NOT_PRIMARY        0x0100 /* 256 */
14 14
 #define BAD_READ_QUALITY   0x0200 /* 512 */
15 15
 #define DUPLICATE_READ     0x0400 /* 1024 */
16
+#define SUPPLEMENTARY      0x0800 /* 2048 */
16 17
 
17 18
 /* 83 = first read, minus strand for paired */
18 19
 /* 99 = first read, plus strand for paired */
... ...
@@ -22,28 +23,5 @@
22 23
 /* For forcing a read to be primary */
23 24
 #define SET_PRIMARY        0xFEFF /* do a logical-and (&) with this */
24 25
 
25
-
26
-/* XO tag for output type */
27
-#define ABBREV_NOMAPPING_1 "N1"
28
-#define ABBREV_NOMAPPING_2 "N2"
29
-#define ABBREV_HALFMAPPING_UNIQ "HU"
30
-#define ABBREV_HALFMAPPING_CIRCULAR "HC"
31
-#define ABBREV_HALFMAPPING_TRANSLOC "HT"
32
-#define ABBREV_HALFMAPPING_MULT "HM"
33
-#define ABBREV_UNPAIRED_UNIQ "UU"
34
-#define ABBREV_UNPAIRED_CIRCULAR "UC"
35
-#define ABBREV_UNPAIRED_TRANSLOC "UT"
36
-#define ABBREV_UNPAIRED_MULT "UM"
37
-#define ABBREV_PAIRED_UNIQ_CIRCULAR "PC"
38
-#define ABBREV_PAIRED_UNIQ_INV "PI"
39
-#define ABBREV_PAIRED_UNIQ_SCR "PS"
40
-#define ABBREV_PAIRED_UNIQ_LONG "PL"
41
-#define ABBREV_PAIRED_MULT "PM"
42
-#define ABBREV_CONCORDANT_UNIQ "CU"
43
-#define ABBREV_CONCORDANT_CIRCULAR "CC"
44
-#define ABBREV_CONCORDANT_TRANSLOC "CT"
45
-#define ABBREV_CONCORDANT_MULT "CM"
46
-
47
-
48 26
 #endif
49 27