sync mpertea/stringtie2 changes

gpertea · gpertea · commit d84cf1d31674 · 2019-07-20T12:06:11.000-04:00
diff --git a/README.md b/README.md
@@ -4,8 +4,8 @@ In order to build StringTie from this GitHub repository
 the following steps can be taken:
  
 ```
-git clone https://github.com/gpertea/stringtie
-cd stringtie
+git clone https://github.com/mpertea/stringtie2
+cd stringtie2
 make release
 ```
 
@@ -14,12 +14,34 @@ which is more suitable for debugging and runtime checking but which can be
 significantly slower than the optimized version which is obtained by using 
 `make release`.
 
+
+### Installation of the super-reads module (optional)
+
+This optional module can be used to de-novo assemble, align and pre-process
+RNA-Seq reads, preparing them to be used as "super-reads" by Stringtie.
+
+Mode detailed information is provided in the SuperReads_RNA/README.md 
+Quick installation instructions for this module (assuming the above Stringtie installation 
+was completed):
+
+```
+ cd SuperReads_RNA
+ ./install.sh
+```
+
+#### Using super-reads with Stringtie
+
+After running the super-reads module (see the SuperRead_RNA/README.md file for usage details), there 
+is a BAM file which contains sorted alignment for both short reads and super-reads, called *`sr_merge.bam`*, 
+created in the selected output directory. This file can be directly given as the main input file
+to StringTie as described in the _Running Stringtie_ section below.
+
 ## Running StringTie
 
 Run stringtie from the command line like this:
-'''
+```
 stringtie [options] <aligned_reads.bam>
-'''
+```
 The main input of the program is a SAMTools BAM file with RNA-Seq mappings
 sorted by genomic location (for example the accepted_hits.bam file produced
 by TopHat).
@@ -84,7 +106,6 @@ the following options are available:
 
 ## Input files
 
-
 StringTie takes as input a binary SAM (BAM) file sorted by reference position. 
 This file contains spliced read alignments such as the ones produced by TopHat or HISAT2.
 A text file in SAM format should be converted to BAM and sorted using the 
@@ -103,10 +124,13 @@ records. For example HISAT2 should be run with the `--dta` option in order to ta
 alignments this way. As explained above, the alignments in SAM format should be sorted and
 preferrably converted to BAM.
 
-Optionally, a reference annotation file in GTF/GFF3 format can be provided to StringTie. 
-In this case, StringTie will check to see if the reference transcripts are expressed in the 
-RNA-Seq data, and for the ones that are expressed it will compute coverage and FPKM values.
-Note that the reference transcripts need to be fully covered by reads in order to be included
-in StringTie's output. Other transcripts assembled from the data by StringTie and not present
-in the reference file will be printed as well ("novel" transcripts).
+Optionally, a reference annotation file in GTF/GFF3 format can be provided to StringTie 
+using the `-G` option. In this case, StringTie will check to see if the reference transcripts 
+are expressed in the RNA-Seq data, and for the ones that are expressed it will compute coverage
+and FPKM values.
+Note that the reference transcripts should be fully covered by reads in order to be included
+in StringTie's output with the original ID of the reference transcript shown in the 
+_`reference_id`_ GTF attribute in the output file . Other transcripts assembled from 
+the input alignment data by StringTie and not present in the reference file will be 
+printed as well ("novel" transcripts).
 
diff --git a/prep_linux.sh b/prep_linux.sh
@@ -13,10 +13,10 @@ mkdir $linpack
 cd $srcpack
 make cleanall
 make static
-cp LICENSE README stringtie ../$linpack/
+cp LICENSE README.md run_tests.sh stringtie ../$linpack/
 cd ..
 tar cvfz $linpack.tar.gz $linpack
 ls -l $linpack.tar.gz
 echo "scp $linpack.tar.gz $srcpack.tar.gz  salz:~/html/software/stringtie/dl/"
-echo "If you're on salzN machines you can also update the release# links:"
+echo "If you're on CCB servers you can also update the release# links:"
 echo "perl -i -pe 's/stringtie\-\d\.\d+\.\d+\w?\./stringtie-$ver./g' ~/html/software/stringtie/home.shtml"
diff --git a/prep_mac.sh b/prep_mac.sh
@@ -11,7 +11,7 @@ echo "-------------------"
 mkdir $macpack
 make clean
 make release
-cp -p LICENSE README stringtie $macpack/
+cp -p LICENSE README.md run_tests.sh stringtie $macpack/
 tar cvfz $macpack.tar.gz $macpack
 ls -l $macpack.tar.gz
 #echo "If you're on igmN machines you can also update the web files:"
diff --git a/prep_source.sh b/prep_source.sh
@@ -13,13 +13,11 @@ cd samtools-0.1.18
 make clean
 cd ..
 libdir=stringtie-$ver/gclib/
-cp Makefile LICENSE README stringtie.cpp {rlink,tablemaker,tmerge}.{h,cpp} $pack/
-#sed 's|\.\./gclib|./gclib|' Makefile > $pack/Makefile
+cp Makefile LICENSE README.md run_tests.sh stringtie.cpp {rlink,tablemaker,tmerge}.{h,cpp} $pack/
 cp -r samtools-0.1.18 $pack/
 /bin/rm -rf $pack/samtools-0.1.18/.svn
 cp ./gclib/{GVec,GList,GHash,GIntHash}.hh $libdir
 cp ./gclib/GBitVec.h $libdir
 cp ./gclib/{GArgs,GBam,GBase,gdna,GStr,gff,codons,GFaSeqGet,GFastaIndex,proc_mem,GThreads}.{h,cpp} $libdir
 tar cvfz $pack.tar.gz $pack
 ls -l $pack.tar.gz
-#scp $pack.tar.gz igm3:~/src/
diff --git a/run_tests.sh b/run_tests.sh
@@ -42,7 +42,9 @@ for i in ${!arrmsg[@]}; do
    echo "Error: file $fcmp does not exist! Re-download test data."
    exit 1
  fi
- echo "Test ${i}: ${arrmsg[$i]}"
+ n=$i
+ ((n++))
+ echo "Test ${n}: ${arrmsg[$i]}"
  fin=${arrins[$i]}.bam
  ../stringtie ${arrparms[$i]} -o $fout $fin
  if [ ! -f $fout ]; then
