update for issue #14

migrated to maven build system, needed to modify the imports for several fixed a bug that caused an error in the calculateConfidence method due to a list indexing error

The calculateConfidence method was improperly formulated so that confidence values >1 were reported when the '-c' parameter >= 1. Now the '-c' parameter is deprecated so that confidence values are reported in the proper range (0-1.0).

files, and removed deprecated usage of samfilereader in htsjdk

added scm to pom

logs IsoSCM-version during execution

logs written to a single generic log so it does not need to wait for
command to be parsed to begin logging

deleted lib folders and jars

removed extra eclipse files that were being tracked

fix for numerical overflow during enumerate

when performing the enumerate command the integer used to count isoforms can potentially overflow, resulting in the -max_isoforms argument not being correctly respected (see #10). I've replaced the integer variable with a BigInteger to avoid these overflow issues.

There were also some lingering "null" labeled junctions relating to issue #10, these remaining cases appear to be due to 1nt long introns implied by aligned reads. While a 1nt intron doesn't make much sense (a 1nt deletion is probably more likely), IsoSCM delegates to the aligner to identify intron positions correctly. As such, if 1nt introns are reported by the aligner, they are now handled by IsoSCM incorporated into resulting gene models without null labels.

patch for issue #10

this revision addresses issue #10 in which some splice junctions recieve "null"
labels, which caused the enumerate function to run incorrectly.

This issue labeling junctions occured because the aligner (STAR)
assigned the read a strand flag (XS) that conflicted with the strand
implied by the sequencing protocol.

This patch modifies IsoSCM such that splice junctions from reads with
conflicting strand information are omitted from assembled transcript
models.

added 'diff' command

added a 'diff' command to identify annotated loci that are overlapped by differential exon isoforms identified by the IsoSCM 'compare' command, a feature requested in issue #7

fix for issue #7

this corrects a bug in the 'compare' command when the results from the 'assemble' step are located in different directories.

fix for issue #5

this release fixes an error that happens when the cigar string contains a deletion immediately prior to the intron.

patch for error in confidence calculation

an error caused by an array out of bounds exception during the confidence calculation is corrected

patch for splice junction counting error

this patches a rare error that occurs when the last read aligned to a reference sequence contains a splice junction

version 2.0.0 released

• Modified the command line interface to save parameters and streamline analysis via configuration files
• Added command line parameter validation and error messages
• Added log messages
• Confidence estimate for change-point
• Added enumerate command to output transcript models in GTF format
• Modified tabular output for compare command

IsoSCM version 1.0.0 is released!

The initial release contains functionality for transcript assembly in single samples and identification of differentially used tandem polyadenylation sites between pairs of samples.