added tests for find_SNPs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1510 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/find_SNPs.in b/bp_test/in/find_SNPs.in
new file mode 100644 (file)
index 0000000..5f4ffc8
--- /dev/null
+++ b/bp_test/in/find_SNPs.in
@@ -0,0 +1,60 @@
+MAPQ: 37
+STRAND: -
+Q_ID: ID00002249
+ALIGN: 63:->A
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 2937
+SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC
+CIGAR: 63M1I36M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00004198
+ALIGN: 8:G>C
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 993
+SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
+CIGAR: 100M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00004198
+ALIGN: 8:G>C
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 993
+SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
+CIGAR: 100M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---

diff --git a/bp_test/out/find_SNPs.out.1 b/bp_test/out/find_SNPs.out.1
new file mode 100644 (file)
index 0000000..f92cd4f
--- /dev/null
+++ b/bp_test/out/find_SNPs.out.1
@@ -0,0 +1,81 @@
+MAPQ: 37
+STRAND: -
+Q_ID: ID00002249
+ALIGN: 63:->A
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 2937
+SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC
+CIGAR: 63M1I36M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00004198
+ALIGN: 8:G>C
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 993
+SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
+CIGAR: 100M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00004198
+ALIGN: 8:G>C
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 993
+SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
+CIGAR: 100M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---
+MAPQ: 37
+STRAND: -
+Q_ID: ID00009237
+ALIGN: 61:G>-
+S_ID: gi|48994873|gb|U00096.2|
+REC_TYPE: SAM
+S_BEG: 5440
+SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
+CIGAR: 61M1D39M
+---
+REC_TYPE: SNP
+S_ID: gi|48994873|gb|U00096.2|
+POS: 632937
+EVENT: ->A
+SNP_COUNT: 1
+TYPE: INSERTION
+---
+REC_TYPE: SNP
+S_ID: gi|48994873|gb|U00096.2|
+POS: 8993
+EVENT: G>C
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|48994873|gb|U00096.2|
+POS: 615440
+EVENT: G>-
+SNP_COUNT: 3
+TYPE: DELETION
+---

diff --git a/bp_test/test/test_find_SNPs b/bp_test/test/test_find_SNPs
new file mode 100755 (executable)
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_find_SNPs
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean